diff --git a/.travis.yml b/.travis.yml
index 6e1b18692df3a320574ce4a3a8ae7bc5063c01f0..f9a634a735d4259642a46f51a4a20060e82a811c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,13 +4,13 @@ jdk:
sudo: true
env:
global:
- - BUILD_CMD='mvn -X -Dskip.tests=true validate clean install'
- - RUN_TESTS=false
+ - BUILD_CMD='mvn -Dskip.tests=true clean package'
+ - RUN_TESTS=true
matrix:
include:
- jdk: oraclejdk8
env:
- - RUN_TESTS=false
+ - RUN_TESTS=true
cache:
directories:
- "${HOME}/dependencies"
@@ -19,7 +19,7 @@ before_install:
- "export DISPLAY=:99.0"
- "sh -e /etc/init.d/xvfb start"
- "source install_dependencies.sh"
- - mvn -X validate
+ - mvn validate
install:
- "$BUILD_CMD"
script:
diff --git a/README.md b/README.md
index e4108f4dfa83dae5cde153855892c4de6afbae67..9880bc1e301bdf8a6f243b463f05640b3e8bf290 100644
--- a/README.md
+++ b/README.md
@@ -33,13 +33,19 @@ ACT is a free tool for displaying pairwise comparisons between two or more DNA s
For further information, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
-## Installation
+## Installation and Usage
-For instructions on how to install Artemis, please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf).
+Please refer to the relevant documentation in the Documentation section below.
-## Usage
+## Building the Applications From Scratch
-For instructions please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf)
+If you would prefer to build the applications from scratch rather than use the pre-built releases in GitHub, then you will firstly need the source code from GitHub. This can be obtained by cloning the repository:
+
+git clone http://github.com/sanger-pathogens/Artemis.git
+
+or by downloadng the source zip file for a particular release. Apache Maven and Java 8 will need to be installed beforehand, in order to build. The applications can be built by issuing the following command in the top-level folder:
+
+mvn validate clean test package
## License
Artemis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/artemis/blob/master/LICENSE).
@@ -49,15 +55,13 @@ For more information on how to download Artemis, please see the [Artemis GitHub
## Documentation
The Artemis user manual is at:
- http://www.sanger.ac.uk/science/tools/artemis
+ http://sanger-pathogens.github.io/Artemis/Artemis/
The ACT user manual is at:
- http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
-
-The DNA plotter user manual is at:
- http://www.sanger.ac.uk/science/tools/dnaplotter
-
-The BAM View user manual is at:
- http://www.sanger.ac.uk/science/tools/bamview
-
+ http://sanger-pathogens.github.io/Artemis/ACT/
+
+The DNA plotter documentation is at:
+ http://sanger-pathogens.github.io/Artemis/Artemis/DNAPlotter/
+The BAM View documentation is at:
+ http://sanger-pathogens.github.io/Artemis/Artemis/BamView/
diff --git a/act b/act
index 0959877a4004caad2fe984c27eab6bd9efa6586e..02cd51e223fb51dbae2891baca22b3df3aa9022a 100755
--- a/act
+++ b/act
@@ -138,7 +138,7 @@ then
echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
result=$?
exit $result
diff --git a/art b/art
index 906ea68523ce25eba136014ad5c957f74f99f78a..f3413f1e633e634a1596e1a579a9c36262b37182 100755
--- a/art
+++ b/art
@@ -144,7 +144,7 @@ then
echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
result=$?
exit $result
diff --git a/bamview b/bamview
index d47b8d94ef8f31535f9ce350c8d5dba52363caae..30b8d603d9f82bc24967cfe51b0093e0d429140e 100755
--- a/bamview
+++ b/bamview
@@ -82,7 +82,7 @@ then
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
result=$?
exit $result
diff --git a/dnaplotter b/dnaplotter
index df5e976dd0204dea90bac4b401d8edc6c2d082f6..a0f36b4c046da8f7f4157c0c635176b48d5960c6 100755
--- a/dnaplotter
+++ b/dnaplotter
@@ -119,7 +119,7 @@ then
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
result=$?
exit $result
diff --git a/docs/chado/ACT.html b/docs/chado/ACT.html
deleted file mode 100644
index 242cce92835aac727f19eb9f25a629d5ff90672b..0000000000000000000000000000000000000000
--- a/docs/chado/ACT.html
+++ /dev/null
@@ -1,27 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"/>
-<title>Artemis - Chado tutorial</title>
-
-</head>
-<body>
-
-<h2>Generating ACT Comparison File</h2>
-
-<p>BLAST is used to generate the ACT comparison file (for more details see the <a href="http://www.sanger.ac.uk/Software/ACT/">ACT manual</a>) one of the
-sequences needs to be made the database sequence and indexed with formatdb:
-</p><pre>formatdb -i NC_004314.fasta -p 'F'
-</pre>
-<p>The other sequence is the query and you can then search for matches between these:
-</p>
-<pre>blastall -p tblastx -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_tblastx -m 8
-</pre><p>or
-</p>
-<pre>blastall -p blastn -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_blastn -m 8 -e 0.1
-</pre>
-<p>Use the '-m 8' option to provide the tabular output that ACT uses.
-</p><p>An alternative to this is to use <a href="http://www.webact.org">WebACT</a> or <a href="http://www.hpa-bioinfotools.org.uk/pise/double_act.html">Double ACT</a> to generate the comparison file.
-</p>
-</body>
-</html>
diff --git a/docs/chado/ActSelection.gif b/docs/chado/ActSelection.gif
deleted file mode 100644
index b9e313388442e413c56d10cc877a02c5f45b7e65..0000000000000000000000000000000000000000
Binary files a/docs/chado/ActSelection.gif and /dev/null differ
diff --git a/docs/chado/ActSelection2seqs.gif b/docs/chado/ActSelection2seqs.gif
deleted file mode 100644
index 5503015ab8040046b96e985efe03f51f34db01d0..0000000000000000000000000000000000000000
Binary files a/docs/chado/ActSelection2seqs.gif and /dev/null differ
diff --git a/docs/chado/AddCV.gif b/docs/chado/AddCV.gif
deleted file mode 100644
index 27e3bbc8a3066fd10088f0bb45becb57591af9dd..0000000000000000000000000000000000000000
Binary files a/docs/chado/AddCV.gif and /dev/null differ
diff --git a/docs/chado/Artemis.gif b/docs/chado/Artemis.gif
deleted file mode 100644
index 7da2adf240f12e627156f40c752506c683c95e35..0000000000000000000000000000000000000000
Binary files a/docs/chado/Artemis.gif and /dev/null differ
diff --git a/docs/chado/ArtemisLogin.gif b/docs/chado/ArtemisLogin.gif
deleted file mode 100644
index fd7cec95197bf544692852506eaf9a01024511fc..0000000000000000000000000000000000000000
Binary files a/docs/chado/ArtemisLogin.gif and /dev/null differ
diff --git a/docs/chado/CV.gif b/docs/chado/CV.gif
deleted file mode 100644
index 7e2c3924e866295960c73acfae57fa1e90445047..0000000000000000000000000000000000000000
Binary files a/docs/chado/CV.gif and /dev/null differ
diff --git a/docs/chado/GMOD2009SummerSchool.shtml b/docs/chado/GMOD2009SummerSchool.shtml
deleted file mode 100644
index 79473ed0cc6448843eefdf85ecfd220c75870f99..0000000000000000000000000000000000000000
--- a/docs/chado/GMOD2009SummerSchool.shtml
+++ /dev/null
@@ -1,331 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" dir="ltr">
- <head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta name="keywords" content="Artemis, Chado, ACT" />
-
- <title>GMOD : Artemis Chado Set Up Tutorial</title>
- </head>
-<body>
-
-<a name="Contents"></a><h2>Contents</h2>
-<ul>
-<li> <a href="#Overview" title="">Overview</a></li>
-<li> <a href="#Download_and_Install_Postgres" title="">Download and Install Postgres</a>
-</li><li> <a href="#Download_and_Install_Chado" title="">Download and Install Chado</a>
-</li><li> <a href="#Examples_of_Loading_Sequences_into_the_Database" title="">Examples of Loading Sequences into the Database</a>
-
-</li><li> <a href="#Download_Artemis_and_ACT" title="">Download Artemis and ACT</a>
-</li><li> <a href="#Running_Artemis" title="">Running Artemis</a>
-</li><li> <a href="#Configuration_Options" title="">Configuration Options</a>
-</li><li> <a href="#Adding_Controlled_Vocabulary_Qualifiers_in_the_Artemis_Gene_Builder" title="">Adding Controlled Vocabulary Qualifiers in the Artemis Gene Builder</a>
-</li><li> <a href="#Transfer_Annotation_Tool_.28TAT.29" title="">Transfer Annotation Tool (TAT)</a>
-</li><li> <a href="#Logging_Information" title="">Logging Information</a>
-
-</li><li> <a href="#Running_ACT" title="">Running ACT</a>
-</li><li> <a href="#Writing_Out_Sequence_Files" title="">Writing Out Sequence Files</a>
-</li><li> <a href="#Mailing_List" title="">Mailing List</a>
-</li><li> <a href="#References" title="">References</a>
-</li></ul>
-
-<a name="Overview"></a><h2>Overview</h2>
-<p>In this tutorial we present how to install and configure
-<a href="http://www.sanger.ac.uk/Software/Artemis/">Artemis</a> and
-<a href="http://www.sanger.ac.uk/Software/ACT/">ACT</a> to use with a
-Chado database. The first two sections relate to installing Postgres
-and Chado, this is included for completeness only and you should refer
-to the Chado session for more details on this.
-
-</p>Artemis is a DNA sequence browser which works with flat files (e.g. EMBL, GenBank, GFF) and more recently with Chado databases. ACT (Artemis Comparison Tool) is based on Artemis. ACT uses BLAST comparison files to highlight regions of interest between pairs of sequences. Artemis and ACT in database mode are increasingly being used in the Pathogen Genomics Group at the Sanger Institute.
-</p>
-
-
-<a name="Download_and_Install_Postgres"></a><h2>Download and Install Postgres</h2>
-
-<pre>./configure --prefix=/home/gmod/gmod_test/pgsl --with-pgport=5432 --with-includes=/Developer
-make
-make install
-
-cd /home/gmod/gmod_test/pgsl
-bin/initdb -D data/
-</pre>
-<p>Added the line to data/postgresql.conf:
-</p>
-<pre>listen_addresses = 'localhost'
-</pre>
-<p>Create the database:
-</p>
-<pre>postmaster -D data &
-createuser --createdb username
-createlang plpgsql template1
-createdb --port=5432 chado_pathogen
-</pre>
-<a name="Download_and_Install_Chado"></a><h2>Download and Install Chado</h2>
-
-<ul><li> Download stable release (gmod-1.0.tar.gz)
-</li><li> Install BioPerl (<a href="http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix" class="external free" title="http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix" rel="nofollow">http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix</a>)
-</li><li> Install go-perl <a href="http://search.cpan.org/~cmungall/go-perl/" class="external free" title="http://search.cpan.org/~cmungall/go-perl/" rel="nofollow">http://search.cpan.org/~cmungall/go-perl/</a>
-</li><li> Install BioPerl (<a href="http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix" class="external free" title="http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix" rel="nofollow">http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix</a>)
-</li><li> Install go-perl <a href="http://search.cpan.org/~cmungall/go-perl/" class="external free" title="http://search.cpan.org/~cmungall/go-perl/" rel="nofollow">http://search.cpan.org/~cmungall/go-perl/</a>
-
-</li><li> Install Bundle::GMOD from cpan
-</li></ul>
-<pre>export GMOD_ROOT=/usr/local/gmod CHADO_DB_NAME=chado_pathogen CHADO_DB_USERNAME=username CHADO_DB_PORT=5432
-</pre>
-<p>Now compile Chado and install the standard components (schema and ontologies):
-</p>
-<pre>perl Makefile.PL
-make
-sudo make install
-make load_schema
-make prepdb
-make ontologies
-</pre>
-<a name="Examples_of_Loading_Sequences_into_the_Database">
-</a><h2>Examples of Loading Sequences into the Database</h2>
-<p>In this section we detail how to load 3 Plasmodium sequences into Chado for viewing in Artemis and ACT. Alternatively you can use your own sequences of interest.
-</p><p>The GenBank files are available from Entrez with the links below. Make sure you download it with the sequence by clicking on the option 'Show sequence' and 'Update View'. Then go to the Download menu and select GenBank(Full):
-
-</p>
-<ul><li> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term=NC_004314" class="external text" title="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term=NC_004314" rel="nofollow">NC_004314</a> (Plasmodium falciparum 3D7 chromosome 10)
-</li><li> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term=NC_011907" class="external text" title="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term=NC_011907" rel="nofollow">NC_011907</a> (Plasmodium knowlesi chromosome 6) and
-</li><li> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term=NC_011909" class="external text" title="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term=NC_011909" rel="nofollow">NC_011909</a> (Plasmodium knowlesi chromosome 8).
-</li></ul>
-<p>These are usually downloaded to the Desktop directory (depending on the browser). They are saved as something like sequences.gbwithparts. Re-name them as NC_004314.gbk, NC_011907.gbk and NC_011909.gbk. Pfalciparum and Pknowlesi will need to be added to your organism table in Chado.
-</p>
-<pre> psql chado_pathogen
-</pre>
-
-<pre class="code"> <span style="color:red">INSERT INTO</span> organism
- ( abbreviation, genus, species, common_name )
- <span style="color:red">VALUES</span>
- ( 'Pfalciparum', 'Plasmodium', 'falciparum', 'Pfalciparum'),
- ( 'Pknowlesi', 'Plasmodium', 'knowlesi', 'Pknowlesi');</pre>
-
-<p>Using the perl script 'bp_genbank2gff3.pl' to convert the GenBank files to GFF3 format:
-</p>
-<pre>bp_genbank2gff3.pl -noCDS *.gbk
-</pre>
-<p>You need to modify the gff files so that the correct SO term is used:
-</p>
-<pre>perl -pi~ -e s'|processed_transcript|mature_transcript|' *.gff
-</pre>
-<p>Then load the GFF3 files that have been created:
-</p>
-<pre>gmod_bulk_load_gff3.pl -organism Pfalciparum -dbname chado_pathogen \
- -dbuser gmod -dbport 5432 -dbpass dd -recreate_cache < NC_004314.gbk.gff
-
-gmod_bulk_load_gff3.pl -organism Pknowlesi -dbname chado_pathogen \
- -dbuser gmod -dbport 5432 -dbpass dd -recreate_cache < NC_011907.gbk.gff
-
-gmod_bulk_load_gff3.pl -organism Pknowlesi -dbname chado_pathogen \
- -dbuser gmod -dbport 5432 -dbpass dd -recreate_cache < NC_011909.gbk.gff
-
-</pre>
-<a name="Download_Artemis_and_ACT"></a><h2>Download Artemis and ACT</h2>
-<p>You can download <a href="http://www.sanger.ac.uk/Software/Artemis/" class="external text" title="http://www.sanger.ac.uk/Software/Artemis/" rel="nofollow">Artemis</a> and <a href="http://www.sanger.ac.uk/Software/ACT/" class="external text" title="http://www.sanger.ac.uk/Software/ACT/" rel="nofollow">ACT</a> from their home pages at the Sanger Institute. For the most up-to-date developments download the software from the CVS server:
-</p>
-<pre>cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/pathsoft co artemis
-</pre>
-<p>Now compile the software:
-</p>
-<pre>cd artemis
-make
-</pre>
-<p>Or download the development version from the <a href="http://www.sanger.ac.uk/Software/Artemis/#development" class="external text" title="http://www.sanger.ac.uk/Software/Artemis/#development" rel="nofollow">Development section</a> on the Artemis home page. Note that on the Artemis web site there is also a <a href="http://www.sanger.ac.uk/Software/Artemis/stable/" class="external text" title="http://www.sanger.ac.uk/Software/Artemis/stable/" rel="nofollow">stable</a> release available.
-</p>
-<a name="Running_Artemis"></a><h2>Running Artemis</h2>
-
-<p>Try running the 'art' script in the download:
-</p>
-<pre>./art -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis
-</pre>
-<p>This opens the login window:
-</p><p>
-<a href="ArtemisLogin.gif" class="image" title="Artemis Login"><img alt="Image:ArtemisLogin.gif" src="ArtemisLogin.gif" width="550" height="253" border="0" /></a>
-</p><p>
-The Artemis Database Manager and File Manager will open once your login has been authenticated. The top part of this relates to the Chado database and the bottom comprises the file management:
-</p><p>
-<a href="databasemanager.gif" class="image" title="Database Manager"><img alt="Image:DatabaseManager.gif" src="databasemanager.gif" width="434" height="867" border="0" /></a>
-</p><p>
-Select the sequence NC_004314 and double click on it to open it up in Artemis.
-</p><p>
-<a href="Artemis.gif" class="image" title="Artemis"><img alt="Artemis.gif" src="Artemis.gif" width="900" height="700" border="0" /></a>
-</p><p>
-There are 3 main components to the Artemis window. The two top Feature Displays show the sequence at different levels of granularity and below these is a feature list:
-
-</p>
-<ol><li> the <b>top Feature Display</b> is a zoomed out view of the sequence. The 3 forward and 3 reverse frames of translation are show with stop codons marked as black vertical lines.
-</li><li> the <b>second Feature Display</b> shows the sequence at the nucleotide level. The amino acid translations are seen in this view.
-</li><li> the <b>Feature List</b> shows the feature types and location. Options for displaying user defined qualifiers (e.g. Dbxref) can be accessed by right clicking on this list and selecting "Show Selected Qualifiers".
-</li></ol>
-
-<p>These three components are connected, so that if you select a feature in one then that feature becomes selected in the others. Double clicking on the feature centers the feature in both feature displays. The scroll bars on the right hand side of the feature displays allow you to zoom in and out.
-</p><p>The alternative way to open your sequence is to provide the entry (e.g. Pfalciparum:NC_004314) you want to open as a command line argument:
-</p>
-<pre> ./art -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis \
- Pfalciparum:NC_004314
-</pre>
-<p>For any of the gene features in Artemis you can select them and press the short cut key 'E' (Edit->Selected Features in Editor). This opens up the Gene Builder. Within this the Gene Model can be edited and annotation added.
-</p><p>
-<a href="genebuilder.gif" class="image" title="GeneBuilder"><img alt="GeneBuilder" src="genebuilder.gif" width="760" height="921" border="0" /></a>
-</p>
-
-<a name="Configuration_Options"></a><h2>Configuration Options</h2>
-<p>Edit 'etc/options' (to change settings globally) or create a file ~/.artemis_options in your home directory (for your own settings). There are various flags that can be used to configure Artemis and ACT with Chado.
-</p><p><b>chado_servers</b> This allows you to provide a list of available servers for the user to select:
-</p>
-<pre>chado_servers = \
- Plasmodium localhost:5432/chado_pathogen?username \
- GeneDB db.genedb.org:5432/snapshot?genedb_ro
-</pre>
-
-<p><b>product_cv</b> In the Pathogen Genomics Group the product qualifiers are stored as an ontology (as a cv in feature_cvterm). This can be changed so that they are stored as featureprop's by setting the product_cv option:
-</p>
-<pre>product_cv=no
-</pre>
-<p>This will mean that the product will be shown in the "Core" section of the Artemis Gene Builder rather than the "Controlled Vocabulary" section.
-</p><p><b>synonym_cvname</b> If synonym types are loaded into a CV, Artemis checks this ontology.
-</p><p><b>set_obsolete_on_delete</b> This will set the default behaviour of Artemis when features are deleted. If set to:
-</p>
-<pre>set_obsolete_on_delete=yes
-</pre>
-<p>the features will be made obsolete. The user is still prompted with the option to permanently delete the feature. If this line is not in the option file the default is to permanently delete features.
-
-</p><p><b>Selecting an alternative gene model</b> Artemis supports 2 types of gene model representations:
-</p><p>A) Pathogen Genomics Gene Model - implicit CDS + explicit UTRs
-</p>
-<pre> gene
- |
- |- part_of mRNA
- |
- |---- part_of exon
- |
- |---- derives_from polypeptide
- |
- |---- part_of five_prime_UTR
- |
- |---- part_of three_prime_UTR
-
-</pre>
-<p>B) implicit CDS + UTRs
-</p>
-<pre> gene
- |
- |- part_of mRNA
- |
- |---- part_of exon
- |
- |---- derives_from polypeptide
-</pre>
-<p>The Artemis default is model A. To use model B then set:
-</p>
-<pre>chado_infer_CDS_UTR=yes
-</pre>
-
-<p><b>sequence_update_features</b> This lists the features that Artemis will maintain the feature.residue column for. This is generally useful for polypeptide and transcript features.
-</p>
-<a name="Artemis_Database_Manager"></a><h2>Artemis Database Manager</h2>
-<p>The database manager provides the list of organisms that have features with residues (currently Artemis searches for these on features of type: '*chromosome*', '*sequence*', 'supercontig', 'ultra_scaffold', 'golden_path_region', 'contig'). The database manager is cached between sessions (this is on by default and can be switched off with -Ddatabase_manager_cache_off). There is an option under the File menu to clear this cache.
-</p>
-<a name="Adding_Controlled_Vocabulary_Qualifiers_in_the_Artemis_Gene_Builder"></a><h2>
-Adding Controlled Vocabulary Qualifiers in the Artemis Gene Builder</h2>
-
-<p>These use evidence codes which are stored as a feature_cvtermprop's with a type_id which corresponds to a cvterm.name = 'evidence'. There is a useful SQL script (etc/chado_extra.sql) in the Artemis distribution for creating this term in Chado. Run this on the chado_pathogen instance of the database:
-</p>
-<pre>psql -d chado_pathogen -f etc/chado_extra.sql
-</pre>
-<p>(This will also create other terms that are used to store literature (PMID's) qualifiers.)
-</p><p>GO terms can now be selected in the Controlled Vocabulary (CV) section of the Gene Builder and added to features. Additional custom CV's can also be used. For Artemis to recognise it and display it the name of the CV needs to be prefixed by 'CC_'. These then appear in a drop down list when adding CV terms to a feature. Try adding a new CV:
-</p>
-<pre> psql chado_pathogen
-</pre>
-<pre> <span style="color:red">INSERT INTO</span> cv ( name, definition ) <span style="color:red">VALUES</span> ( 'CC_test', 'test' );
-</pre>
-<p>and create a CvTerm in this CV:
-</p>
-<pre> <span style="color:red">INSERT INTO</span> dbxref
- ( db_id, accession )
- <span style="color:red">VALUES</span>
- ( (SELECT db_id FROM db WHERE name = 'CCGEN'), 'test1' );
-</pre>
-<pre> <span style="color:red">INSERT INTO</span> cvterm
- ( cv_id, name, dbxref_id )
- <span style="color:red">VALUES</span>
-
- ( (SELECT cv_id FROM cv WHERE name ='CC_test'), 'test1',
- (SELECT dbxref_id FROM dbxref WHERE accession='test1') );
-</pre>
-<p>Now re-launch Artemis and open the Gene Builder at any feature and go to the 'Controlled Vocabulary' section and click the 'ADD' button. This CV (CC_test) will appear in the drop down menu:
-</p><p>
-<a href="AddCV.gif" class="image" title="Add CV"><img alt="Image:AddCV.gif" src="AddCV.gif" width="284" height="172" border="0" /></a>
-</p><p>
-Click on CC_test and hit the 'Next' button. This opens a keyword selection box. If you leave this blank all the terms are retrieved and displayed. If you keep clicking 'Next' this term is then added to the 'Controlled Vocabulary' section.
-</p><p>
-</p>
-<a name="Transfer_Annotation_Tool_.28TAT.29"></a><h2>Transfer Annotation Tool (TAT)</h2>
-
-<p>This tool can be accessed from the Gene Builder - look for the TAT button. It allows you to transfer annotation between sequences. In database mode Artemis provides an editable list of genes constructed from ortholog/parlog links. These links can be added in the Gene Builder in the Match section (for example you can try creating the ortholog link between PF10_0165 in Pfalciparum and PKH_060110 in Pknowlesi).
-
-</p>
-<a name="Logging_Information"></a><h2>Logging Information</h2>
-<p>Note that you can easily access the logging information Artemis produces. In the Artemis launch window under the 'Options' menu select the 'Show Log Window', this provides the logs. This is controlled by etc/log4j.properties. The logs can be useful for debugging and for monitoring activity if appended to a central file. See the <a href="http://logging.apache.org/log4j/" class="external text" title="http://logging.apache.org/log4j/" rel="nofollow">log4j</a> documentation for more information.
-</p>
-<a name="Running_ACT"></a><h2>Running ACT</h2>
-
-<p>ACT can read sequences in from the database as well. However, it currently does not read the BLAST comparisons from Chado but reads this data from files. These comparisons are displayed as the matches between the sequences. To distinguish forward and reverse matches the forward matches are red and reverse matches are blue.
-</p><p>For convenience the comparison files have been pre-generated for this exercise and can be downloaded from:
-</p>
-<pre><span style="color:red">wget</span> <a href="ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011907_tblastx.gz" class="external free" title="ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011907_tblastx.gz" rel="nofollow">ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011907_tblastx.gz</a>
-<span style="color:red">wget</span> <a href="ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011909_tblastx.gz" class="external free" title="ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011909_tblastx.gz" rel="nofollow">ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011909_tblastx.gz</a>
-</pre>
-<p>Note that both Artemis and ACT automatically open gzipped files. For details on generating these files go to <a href="ACT.html" title="ACT Comparison Files">ACT Comparison Files</a>.
-</p><p>To run ACT use the 'act' script:
-</p>
-
-<pre>./act -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis
-</pre>
-<p>From the 'File' menu select the option 'Open Database and SSH File Manager' and login. Drag and drop the Plasmodium entries from the Database Manager into the ACT selection window. Also, drag and drop the comparison files into this window, so it looks something like this (note the featureId numbers may well be different as these are the Chado feature_id):
-</p><p><br />
-<a href="ActSelection2seqs.gif" class="image" title="Image:ActSelection2seqs.gif"><img alt="Image:ActSelection2seqs.gif" src="ActSelection2seqs.gif" width="528" height="187" border="0" /></a>
-</p><p>
-Click on Apply to read these entries and open up ACT. You can use the right hand scroll bar to zoom in and out. If you zoom out you can indentify the regions that match between these sequences.
-</p><p>
-<a href="Pf10_Pk6.gif" class="image" title="Image:Pf10_Pk6.gif"><img alt="Image:Pf10_Pk6.gif" src="Pf10_Pk6.gif" width="900" height="700" border="0" /></a>
-</p><p>
-ACT can display multiple pairwise comparison. So the two P.knowlesi sequences can be compared to the P.falciparum sequence. From the ACT launch window go to the File menu and select 'Open Database and SSH File Manager'. Drag in the sequences and comparison files (clicking on 'more files' to add the additional sequence and comparison).
-</p><p>
-<a href="ActSelection.gif" class="image" title="Image:ActSelection.gif"><img alt="Image:ActSelection.gif" src="ActSelection.gif" width="528" height="245" border="0" /></a>
-</p><p>
-Zooming out you will see that Pfalciparum chromosome 10 matches to regions in Pknowlesi chromosome 7 and 9.
-</p><p>
-<a href="Pk6_Pf10_Pk8.gif" class="image" title="Image:Pk6_Pf10_Pk8.gif"><img alt="Image:Pk6_Pf10_Pk8.gif" src="Pk6_Pf10_Pk8.gif" width="900" height="700" border="0" /></a>
-
-</p><p>
-</p>
-<a name="Writing_Out_Sequence_Files"></a><h2>Writing Out Sequence Files</h2>
-<p>Artemis can write out EMBL and GFF files for an entry opened from the database. You can optionally flatten the gene model (i.e. gene, transcript, exon) to just a CDS feature. Also an option is given to ignore any obsolete features. For EMBL it uses mappings for conversion of the keys and qualifiers. These mappings are stored in the 'etc/key_mapping' and 'etc/qualifier_mapping' files.
-</p><p>A utility script (etc/write_db_entry) is also provided as a means of writing out multiple sequences from the database. The script takes the following options:
-</p>
-<pre>-h show help
--f [y|n] flatten the gene model, default is y
--i [y|n] ignore obsolete features, default is y
--s space separated list of sequences to read and write out
--o [EMBL|GFF] output format, default is EMBL
--a [y|n] for EMBL submission format change to n, default is y
-</pre>
-<p>Try running:
-</p>
-<pre>etc/writedb_entry -Dchado="localhost:5432/chado_pathogen?gmod" NC_004314
-</pre>
-
-<a name="Mailing_List"></a><h2>Mailing List</h2>
-<p>There is an Artemis mailing list: <a href="http://lists.sanger.ac.uk/mailman/listinfo/artemis-users" class="external text" title="http://lists.sanger.ac.uk/mailman/listinfo/artemis-users" rel="nofollow">artemis-user</a>.
-</p>
-<a name="References"></a><h2>References</h2>
-<p><a href="http://www.sanger.ac.uk/Software/Artemis/" class="external text" title="http://www.sanger.ac.uk/Software/Artemis/" rel="nofollow">Artemis home page</a><br /><a href="http://www.sanger.ac.uk/Software/ACT/" class="external text" title="http://www.sanger.ac.uk/Software/ACT/" rel="nofollow">ACT home page</a><br /><a href="http://www.sanger.ac.uk/Software/Artemis/v11/chado/" class="external text" title="http://www.sanger.ac.uk/Software/Artemis/v11/chado/" rel="nofollow">Artemis Connecting to Chado Databases</a><br /><a href="http://www.sanger.ac.uk/Software/Artemis/v11/database/chado.practical.guide.pdf" class="external text" title="http://www.sanger.ac.uk/Software/Artemis/v11/database/chado.practical.guide.pdf" rel="nofollow">User Practical Guide</a>
-
-</p><p>
-
-</body></html>
-
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-<!--#set var="banner" value="Artemis - Chado Admin/Developer Documentation"-->
-<!--#include virtual="/perl/header"-->
-
-
-<p>
-This page describes some of the development background and admin of
-using and setting up an Artemis and ACT connection with a Chado database.
-
-<ul>
-<li><a href="#DATABASEMANAGER">Opening the Database Manager</a>
-<li><a href="#OPENART">Opening the main Artemis/ACT window</a>
-<li><a href="#CONFIG">Option File Configuration</a>
-<li><a href="#GENEBUILDER">Opening the Standalone Gene Builder</a>
-</ul>
-
-
-
-<h3><a name="DATABASEMANAGER">Opening the Database Manager</a></h3>
-<p>
-The Artemis Database Manager is cached between sessions in the directory
-'.artemis/cache' in the users home directory. There is an option under the File menu
-to clear this cache.
-<p>
-To open the Artemis Database Manager panel (from which the browser is launched),
-Artemis looks initially for the existence of the cvterm.name = 'top_level_seq' which
-belongs to cv.name = 'genedb_misc'. If these exist it follows method A:
-
-<ol type="A">
-<li>
--call 'getTopLevelOrganisms' (in Organism.xml mapping). This relies on the the source
-features (e.g. chromosome) having a featureprop with a type_id corresponding to 'top_level_seq'.
-<p>
-If the 'top_level_seq' is not implemented in the database it then follows method B:
-<p>
-</li>
-
-<li>
--call 'getOrganismsContainingSrcFeatures' (in Organism.xml mapping). This searches for those
-organisms that contain sequences with residues and have a type_id that
-corresponds to a cvterm name that matches:
-<p>
-*chromosome*, *sequence*, supercontig, ultra_scaffold, golden_path_region, or contig
-<p>
-</li>
-</ol>
-When the organisms with the source feature have been identified these are displayed. When
-a user clicks on an organism it opens that node and finds the types (e.g. chromosome, contig) of source
-features and the underlying features that have residues (getResidueFeatures in Feature.xml).
-<p>
-<h3><a name="OPENART">Opening the main Artemis/ACT window</a></h3>
-<p>
-The organismprop's are loaded lazily when a sequence is opened. If an organismprop
-is of type 'translationTable' the value of the organismprop is then used as the
-translation table when Artemis opens a sequence from that organism.
-<p>
-When a sequence is double clicked to open it in Artemis, most things for that sequence
-are read from the database. The iBatis statement calls made when reading an entry are
-summarised below.
-<p>
-<table border=1 cellspacing=1 cellpadding=2>
-<tr><td>Statement ID</td><td>SQL Mapping File</td><td>Description</td></tr>
-<tr><td>getFeature </td><td>(Feature.xml)</td>
- <td>Retrieves all the features and their featureloc's, featureprop's, feature_relationship's and primary dbxref</td></tr>
-<tr><td>getFeatureDbXRefsBySrcFeature </td><td>(FeatureDbXRef.xml)</td>
- <td>Retrieves all secondary dbxref's</td></tr>
-<tr><td>getFeatureSynonymsBySrcFeature </td><td>(FeatureSynonym.xml)</td>
- <td>Retrieves feature synonyms</td></tr>
-<tr><td>getFeatureCvTermsBySrcFeature </td><td>(FeatureCvTerm.xml)</td>
- <td>Retrieves feature_cvterm's, feature_cvtermprop (evidence code, extra qualifiers, date).</td></tr>
-<tr><td>getFeatureCvTermDbXRefBySrcFeature </td><td>(FeatureCvTermDbXRef.xml)</td>
- <td>Retrieves feature_cvterm_dbxref (WITH/FROM column).</td></tr>
-<tr><td>getFeatureCvTermPubBySrcFeature </td><td>(FeatureCvTermPub.xml)</td>
- <td>Retrieves feature_cvterm_pub's.</td></tr>
-</table>
-<p>
-Artemis constructs an internal GFF3 stream from these calls for the selected sequence.
-This is then read in the same way as a GFF3 file as an Artemis DatabaseDocumentEntry
-(which extends GFFDocumentEntry) and creating GFFStreamFeatures.
-<p>
-If the lazy load option is selected from the Database Manager's File menu, then only
-getFeature is called. The resulting GFFStreamFeature object is marked as lazy loading
-and FeatureDbXRefs, FeatureSynonyms, FeatureCvTerms, FeatureCvTermDbXRefs
-and FeatureCvTermPubs are read from the database for a feature when the Gene Builder is opened.
-<p>
-The feature_relationship (from getFeature) is used to create the gene hierarchy; 'part_of'a
-and 'derives_from' relationships become Parent and Derives_from in GFF3 terms. If the
-feature_relationship type_id does not correspond to one of these terms (derives_from,
-part_of, proper_part_of, partof, producedby) then the object_id is recorded as a qualifer
-value. This is used to read orthologous_to and paralogous_to relations. The qualifier
-values for these are lazily stored (as ClusterLazyQualifierValue.java). When Artemis
-displays these qualifiers in the Gene Builder it then queries the database further to
-list the related genes.
-<p>
-Other properties that have a featureloc association with a feature
-are found by calling getLazySimilarityMatches (Feature.xml). Artemis then
-constructs lazy loading qualifiers (QualifierLazyLoading.java) from this that query
-the database further only when that qualifier is needed. This is used for
-blast/fasta similarity and polypeptide_domains.
-
-<p>
-The gene hierarchy is stored internally by the ChadoCanonicalGene.java object and is based
-on the Parent/Derives_from relationships. It stores the related children of the gene.
-The spliced features (exon, pseudogenic_exon) are combined into a single Artemis
-Feature. The joined exons become an Artemis CDS feature (GFFStreamFeature), which stores
-the uniquenames of the original exons in the database.
-
-<p>
-<h3><a name="CONFIG">Artemis Chado Configuration</a></h3>
-
-This is an example extract from the Artemis options file for the chado related options:
-
-<p>
-<pre style="color: #0000FF;">
-#
-# CHADO DATABASE OPTIONS
-#
-# chado gene model features default types
-chado_exon_model=CDS
-#chado_transcript=transcript
-
-# infer CDS and UTR features from gene model
-chado_infer_CDS_UTR=no
-
-# provide a list of available servers
-chado_servers = \
- workshop localhost:10101/workshop?user \
- GeneDB db.genedb.org:5432/snapshot?genedb_ro
-
-# define how product qualifiers are stored (as a cv or as a featureprop)
-product_cv=yes
-product_cvname = genedb_products
-# cv containing synonym names
-synonym_cvname = genedb_synonym_type
-
-# set default delete behaviour to make things obsolete, if
-# this is not provided the default is to permanently delete
-set_obsolete_on_delete=yes
-
-# list of features to record residues for in the database
-# - these are included when inserting or updating their featurelocs
-sequence_update_features = polypeptide mRNA rRNA tRNA snRNA snoRNA
-</pre>
-
-<p>
-Artemis combines the exons stored in chado and describes it as a 'CDS'
-feature by default. The <b>chado_exon_model</b> flag in the options file
-allows this to be changed.
-<p>
-When a gene model is created in Artemis it creates the transcript as a 'mRNA'
-feature by default. The <b>chado_transcript</b> flag in the options file allows this
-to be changed.
-<p>
-For Artemis the default gene model representation is described in the <a href="overview.shtml#GENE">
-overview</a>. In this representation the UTRs are explicitly created in the database.
-However the gmod loader (gmod_bulk_load_gff3.pl) does not create the UTRs and they can
-be inferred from the exon and protein features. If the gmod loader is used then Artemis
-can infer the CDS and UTR features by setting <b>chado_infer_CDS_UTR=yes</b> in the
-options file. Adjusting the polypeptide boundaries in the Gene Builder will result in the generation
-or deletion of UTRs.
-
-<p>
-A list of available databases can be configured in the options file with the <b>chado_servers</b> flag.
-For each database an alias is given followed by its location (host:port/database?user), each alias
-is displayed in a drop down menu in the login box.
-<p>
-If product qualifiers are stored as an ontology (in cvterm) then set <b>product_cv=yes</b>
-and set <b>product_cvname</b> is set to the name of the controlled vocabulary (cv) used in chado.
-<p>
-When features are deleted in Artemis the default behaviour can be set to make these
-features obsolete rather than permanently delete them from the database.
-
-<a name="GENEBUILDER"></a><h3>Opening the Standalone Gene Builder</h3>
-<p>
-The Gene Builder can be launched on its own without opening up Artemis. The following
-opens up a window which lets you type in a gene name to be opened:
-
- <pre>
- java -mx500m -Dibatis -Dchado="localhost:5432/database?" \
- -Djdbc.drivers=org.postgresql.Driver -classpath artemis.jar \
- uk.ac.sanger.artemis.components.genebuilder.GeneEdit
- </pre>
-
-Alternatively the gene name can be given as an argument:
- <pre>
- java -mx500m -Dibatis -Dchado="db.genedb.org:5432/snapshot?genedb_ro" \
- -Djdbc.drivers=org.postgresql.Driver -Dshow_log -Dread_only \
- -classpath jar_build/artemis.jar:etc
- uk.ac.sanger.artemis.components.genebuilder.GeneEdit PFA0010c
- </pre>
-
-
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-<!--#set var="banner" value="Artemis - Chado : Database Loading"-->
-<!--#include virtual="/perl/header"-->
-
-These notes are intended only as a guide and describes an installation carried out on
-a MacOSX (10.5.6). For details on Chado installation see <a href="http://gmod.org">
-gmod.org</a>.
-<ol>
-<li><b>Download and Install Postgres.</b>
-<pre>
-Download postgresql-8.3.5.
-
-./configure --prefix=/Users/tjc/gmod/pgsl --with-pgport=2432 --with-includes=/Developer
-make
-make install
-
-cd /Users/tjc/gmod/pgsl
-bin/initdb -D data/
-
-Added the line to data/postgresql.conf:
-listen_addresses = 'localhost'
-
-bin/postmaster -D data &
-bin/createuser --createdb tim
-bin/createlang plpgsql template1
-bin/createdb --port=2432 test
-</pre>
-</li>
-<li><b>Download and Install Chado.</b> See also the <a href="http://gmod.org/wiki/Chado">
-Chado documentation</a>.
-
-<pre>
-Download stable release (gmod-1.0.tar.gz)
-Install BioPerl (http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix)
-Install go-perl http://search.cpan.org/~cmungall/go-perl/
-
-Install Bundle::GMOD from cpan
-
-setenv GMOD_ROOT /usr/local/gmod
-setenv CHADO_DB_NAME test
-setenv CHADO_DB_USERNAME tim
-setenv CHADO_DB_PORT 2432
-
-Chado installation:
-perl Makefile.PL
-make
-sudo make install
-make load_schema
-make prepdb
-make ontologies
-
-</pre>
-</li>
-<li><b>Examples of Loading Sequences into the Database.</b>
-<p><b>NC_001142:</b><p>
-You may find the following loading fails and you need to insert 'processed_transcript'
-as a sequence ontology cvterm. Or change them to 'mature_transcript' in the gff file
-(e.g. sed s'|processed_transcript|mature_transcript|' NC_001142.gff).
-
-<pre>
-cat NC_001142.gbk | perl /usr/local/bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout > NC_001142.gff
-cat NC_001142.gff | perl /usr/local/bin/gmod_bulk_load_gff3.pl -dbname test -organism "Saccharomyces cerevisiae" -dbuser tim -dbport 2432 -dbpass dd -recreate_cache
-</pre>
-<p><b>NC_008783:</b>
-<p>
-Add this to the organism table:
-<pre>
-INSERT INTO organism
- (abbreviation, genus, species, common_name, organism_id) VALUES
- ('B.bacilliformis', 'Bartonella', 'bacilliformis', 'BB', 8783);
-
-cat NC_008783.gbk | perl /usr/local/bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout > NC_008783.gff
-cat NC_008783.gff | perl /usr/local/bin/gmod_bulk_load_gff3.pl -dbname test -organism "BB" -dbuser tim -dbport 2432 -dbpass dd -recreate_cache
-
-</pre>
-
-Artemis does not (by default) look for sequences that are loaded as a 'region'.
-So change the sequence type of NC_001142 from region to a chromosome:
-<pre>
-UPDATE feature SET
- type_id=(select cvterm_id from cvterm where cv_id=(
- select cv_id from cv where name='sequence') and name='chromosome')
-WHERE uniquename='NC_008783';
-</pre>
-</li>
-<li><b>Run Artemis.</b>
-<pre>
-./art -Dchado="localhost:2432/test?tim" -Dibatis \
- -Djdbc.drivers=org.postgresql.Driver
-</pre>
-<p>If this is successful then the login window will appear and the
-database manager will then open:</p>
-<img src="databasemanager_example.gif" align="middle" alt="databasemanager_example"/>
-
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-<!--#set var="banner" value="Artemis Connecting to Chado Databases"-->
-<!--#include virtual="/perl/header"-->
-
- <a href="http://www.sanger.ac.uk/Software/Artemis/"><b>Artemis</b></a> and
- <a href="http://www.sanger.ac.uk/Software/ACT/"><b>ACT</b></a> can be used
- to connect to <a href="http://www.gmod.org/"><b>Chado</b></a> databases.
- They are being developed to read from and write to the database and perform the
- same functions as the standard Artemis and ACT.
-
- <p>
- An example read-only database can be found
- <a href="http://www.sanger.ac.uk/Software/Artemis/databases/">here</a>.
- <p>
- <h3>Documentation</h3>
- <p>
- <ul>
- <li><a href="overview.shtml">Overview Document</a></li>
- <li><a href="admin.shtml">Admin Document</a></li>
- <li><a href="storage.html">Data Storage</a> (for the Pathogen Group)</li>
- <li><a href="dbloading.shtml">Data Loading Examples</a></li>
- <li><a href="writedb_entry.html">Exporting from the command-line using writedb_entry</a></li>
- </ul>
-
-<p>
-
-<!--#set var="pubmed_tabulate" value="yes"-->
-<!--#set var="pubmed_ids" value="18845581"-->
-<!--#include virtual="/perl/utils/pubmedalizer"-->
-
-
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-<!--#set var="banner" value="Artemis - Chado Overview"-->
-<!--#include virtual="/perl/header"-->
-
- <p>This overview covers:
-
-<ul>
-<li><a href="#CONNECT">Connecting to a Chado Database</a>
-<li><a href="#READ">Reading From the Database</a>
-<li><a href="#IBATIS">iBatis Database Mapping</a>
-<li><a href="#GENE">Gene Representation</a>
-<li><a href="#GENEBUILDING">Gene Building</a>
-<li><a href="#MERGE+SPLIT">Gene merging and splitting</a>
-<li><a href="#TAT">Transfer Annotation Tool</a>
-<li><a href="#WRITE">Writing To The Database</a>
-<li><a href="#GENEBUILDER">Opening the Standalone Gene Builder</a>
-<li><a href="#COMMUNITY+ANNOTATION">Community Annotation</a>
-<li><a href="#WRITING-SEQUENCE-FILES">Writing Out Sequence Files</a>
-</ul>
- <a NAME="CONNECT"></a><h2>Connecting to a Chado Database</h2>
- The following java flags are used when running Artemis when connecting to a
- database. These options currently are all needed.
- <ol>
- <li><b><pre>-Dchado</pre></b>
- this is used to get Artemis to look for the database.
- The address of the database (hostname, port and name) can be conveniently
- included as follows:
- <br><pre>-Dchado="hostname:port/test?username"</pre>
- these details are then the default database address in the popup login window. A
- list of available databases can be provided in the Artemis <a href="admin.shtml#CONFIG">options file</a>
- these are presented in a drop down list in the login window.
- <br><br>
- <img src="login.gif" align="middle" alt="login"/>
- <br>
- </li>
- <li><b><pre>-Djdbc.drivers=org.postgresql</pre></b>
- this is used to define the <a href="http://jdbc.postgresql.org/">
- JDBC postgres driver
- </a>.
- </li>
- <li><b><pre>-Dibatis</pre></b>
- use the <a href="http://ibatis.apache.org/" title="iBatis">iBATIS</a>
- Data Mapper
- </li>
- </ol>
- <br>
- So the command line will look something like this example:
- <pre> ./art -Dchado="localhost:2996/test?tjc" -Dibatis \
- -Djdbc.drivers=org.postgresql.Driver</pre>
-
-For a read only connection -Dread_only is specified on the command line:
- <pre> ./art -Dchado="db.genedb.org:5432/snapshot?genedb_ro" -Dibatis \
- -Djdbc.drivers=org.postgresql.Driver -Dread_only</pre>
-
- <a NAME="READ"></a><h2>Reading From the Database</h2>
- On a successful login a database and file manager window will open up.
- The database manager will display "Database Loading...". The organisms
- in the database with residues are shown in a expandable tree. Double
- clicking on the sequence names opens them up in Artemis. Alternatively
- a gene name or chromosome name came be typed into the text field at the
- top and the Open button used to launch Artemis.
- <br><br>
- <img src="databasemanager.gif"/>
- <p>
- A sequence can be opened in Artemis from the command line (without going
- through the database manager). This is done by supplying a command line argument
- with the organism and chromosome (or source feature):
- <br><pre>Pfalciparum:Pf3D7_09</pre>
- and optionally a range can be included to just display features within it:
- <br><pre>Pfalciparum:Pf3D7_09:92000..112000</pre>
- this could be used in combination with the <i>-Doffset=base</i> flag (<i>e.g.
- -Doffset=10000</i>) to open Artemis at a particular section of a sequence
-
- <p>
- To reduce the number of transactions to the database, all of the sequence is
- read into Artemis. This includes most of the feature qualifiers. There are some
- qualifiers (ortho/paralog and similarity qualifiers) that lazily load their data
- as and when it is needed, <i>i.e.</i> when opened for viewing in the gene builder.
- This lazy loading improves the performance of reading data from the database
- for sequences with a large number of features.
-
-
- <a NAME="IBATIS"></a><h2>iBatis Database Mapping</h2>
- <a href="http://ibatis.apache.org/" title="iBatis">iBatis</a> data mapper
- framework has been used to facilitate the communication with the database
- from Artemis. It uses XML descriptors to couple the SQL statements with the
- Java objects that Artemis understands. The XML maps are in the '<i>artemis_sqlmap</i>'
- in the Artemis distribution. These are divided up into files based on the
- Chado table names.
- <p>
- The SQL statements can be seen in the Artemis <a href=
- "http://www.sanger.ac.uk/Software/Artemis/manual/launch-window.html#LAUNCH-WINDOW-OPTIONS-SHOW-LOG">
- Log Viewer</a> window:<br>
- <img src="logviewer.gif" width="100%"/>
- <br><br>This is mainly useful for debugging and tracking problems with reading
- from and writing to the database. Artemis uses
- <a href="http://logging.apache.org/log4j/">log4j</a> to produce logging
- and the configuration file for this is in the file '<i>etc/log4j.properties</i>'.
-
- <a NAME="GENE"></a><h2>Gene Representation</h2>
- Below is an illustration of how the feature are stored in Chado
- in the Sanger PSU.
- <p>
- <center><b><i>Gene Model</i></b>
- <br>
- <img src="chado_gene_model.gif"/></center>
- <p>The names (in red) are the internal database uniquenames. These names are
- automatically generated by the gene builder from an ID provided by the
- user. <i>N.B.</i> in our data model UTRs are represented as distinct from
- exons.
- <p>
- For the scenario where both the CDS and UTRs are not stored and their positions can be
- inferred from the exon and polypeptide features set <i>chado_infer_CDS_UTR=yes</i> in the
- Artemis <a href="admin.shtml#CONFIG">options file</a>. Adjusting the polypeptide boundaries
- in the Gene Builder will then result in the generation or deletion of UTRs.
- <a NAME="GENEBUILDING"></a><h3>Gene Building</h3>
- A gene can be created in Artemis (or ACT) by highlighting a base range and selecting
- from the '<i>Create</i>' menu the '<i>Gene Model From Base Range</i>' option.
- This prompts for a unique ID and this corresponds to the names in the above
- gene model representation. The basic constituent features are created; <i>i.e.</i>
- gene, transcript, CDS and polypeptide. <i>N.B.</i> Artemis joins the exon
- features and represents them as a CDS feature. These are shown on the frame
- lines in the feature display window.
- <p>
- A gene builder for a selected gene feature can be opened from the '<i>Edit</i>' menu
- by selecting the '<i>Selected Feature in Editor</i>' option or simply using the '<i>E</i>'
- shortcut key.
- <center><p><b><i>The Artemis Gene Builder</i></b><br>
- <img src="editor.gif"></center>
- <p>There are two distinct parts to the gene builder window. The top part shows
- the <b><i>gene hierarchy and structure</i></b>. The bottom part shows the
- <b><i>annotation</i></b> associated with one of the constituent features.
- These two parts of the gene builder are described below.
- <ol>
- <li><b>Gene Hierarchy and Structure</b><br>
- The top left hand side is a tree structure of the gene model. To the right
- of this is a graphical representation of the features. A feature can be selected
- from either the tree or the graphical view. The annotation for the selected
- feature is displayed in the bottom part of the gene builder.
- <p>Structural changes can be carried out in the graphical view. The feature ends
- can be dragged to adjust their coordinates. On right clicking on this area there
- is a popup menu for adding and deleting features in the gene model.
- <center><p><b><i>Editing the Gene Model In the Gene Builder</i></b><br>
- <img src="genebuilder2.gif" border="1"></center>
- <p>
- Additional transcripts can be added from here. The checkbox to the right of
- the above CDS is used to hide and show the associated CDS in the Artemis
- feature display. This can make structural edits clearer for multiple transcripts.
- <p>
- <li><b>Annotation</b><br>
- There are 4 (Properties, Core, Controlled Vocabulary and Match) sections in
- the annotation part of the gene builder. These are described below. These can
- be viewed in a scrollable view or in a tabbed view. There is a check box at
- the bottom of the gene builder to change between these views.
- <p>
- <ul>
- <li><b>Properties</b><br>
- This contains properties such as the synonyms and time last modified. Also
- the ID and Name of the feature are given here, for a gene feature this is
- used as a systematic identifier and a primary name.
- Synonyms are added as a controlled vocabulary (these are in
- a cv named '<i>genedb_synonym_type</i>'). The 'is obsolete' check box is
- used to indicate if this is an obsolete feature. The feature is then marked
- as obsolete in the database. Artemis (by default) does not show obsolete
- features in the feature display and they are shown greyed out in the
- feature list.
-
- <center><p><b><i>Properties section</i></b><br>
- <img src="Properties.gif" border="1"></center>
-
- </li><p>
- <li><b>Core</b><br>
- The core annotation contains any other annotation that does not fit into the
- other sections. <i>E.g.</i> comments, literature, Dbxref. Hyperlinks are
- provided for SWALL, EMBL, UniProt, PMID, PubMed, InterPro and Pfam, and opening
- up a local browser.
- </li><p>
- <li><b>Controlled Vocabulary (CV)</b><br>
- The CV module in Chado is concerned with controlled vocabularies or ontologies.
- Therefore, Chado can use the biological ontologies and this makes it very
- expressive.
- <p>
- This section in the gene builder provides a form for adding and deleting GO,
- controlled curation, product, Riley class annotation. CV terms are added by
- clicking the 'ADD' button. When adding a term to a feature the user is
- prompted for the CV name and then keyword. The term to be added is then
- selected from a drop down list of terms containing the word or phrase.
- To further assist in finding the CV term from the list, typing in the
- text will start to autocomplete and scroll to the first matching term.
-
- <center><p><b><i>CV section</i></b><br>
- <img src="CV.gif" border="1"></center>
-
- <p>GO terms are selected from molecular_function, biological_process
- or cellular_component CV's.
-
- <p>Products are stored in Chado as a CV (<i>i.e.</i> in cvterm in
- a cv named '<i>genedb_products</i>'). They can be given evidence codes
- and have associated WITH/FROM and Dbxref columns.
-
- <p>Other generic controlled curations can be found by Artemis and shown
- if their CV name in Chado is prefixed with '<i>CC_</i>' (<i>e.g.</i>
- CC_controlledcuration, CC_workshop). These then appear in a drop down
- list when adding CV terms to a feature.
-
- <p>Adding new terms to the database can also be done from this section.
- In the drop down selection of CV's there is an 'Add term...' option.
- This opens an input panel for new terms.
- <center><p><b><i>Adding a new CV term</i></b><br>
- <img src="addterm.gif"></center>
- </li><p>
- <li><b>Match</b><br>
- This section allows the user to add ortholog/paralog links to other genes
- in the database.
- <p>
- The ortholog/paralog tables provide links for opening the gene editor or
- an Artemis window for each entry. The '<i>VIEW</i>' button opens a
- separate Artemis displaying the gene ortholog or paralog and the
- surrounding features.
- <p>
- In addition similarity qualifiers can be added here from matches to
- blast and fasta searches carried out in Artemis. These are added
- from the Artemis Object Editor.
- </li>
- </ul>
- </ol>
-
- <a NAME="MERGE+SPLIT"></a><h3>Gene merging and splitting</h3>
-
- To merge gene models, select the CDS segments that are to be merged. Then use
- the menu option:
- <p>
- <pre>Edit->Selected Feature(s)->Merge</pre>
- <p>
- The annotation and names from the segment first selected are maintained and
- the CDS features from the second gene model are added to the first selected gene model.
- The second gene model is deleted automatically.
- <p>
- To unmerge (split) the gene model into two gene models consecutive segments
- in the CDS are selected. This is done by clicking on the first segment and
- then pressing SHIFT and clicking on the second segment. Then use the menu option:
- <p>
- <pre>Edit->Selected Feature(s)->Unmerge</pre>
- <p>
- On unmerging the annotation and synonyms are maintained in both gene models.
- The second gene model component features are given a new internal ID (uniquename)
- based on the original and prefixed with DUP1-.
-
-
- <a NAME="TAT"></a><h3>Transfer Annotation Tool</h3>
- The Transfer Annotation Tool (TAT) within Artemis can be used to transfer annotation
- between features within an EMBL file or features within the same Chado database. It
- is opened by clicking on the "TAT" button in the Feature Editor or, in database mode,
- the Gene Builder.
-
- <center><p><b><i>Transferring Annotation</i></b><br>
- <img src="TAT.gif"></center>
-
- <p>
- The left hand column shows the list of orthologous genes. Features can be added to
- this by clicking the "Add" button and pasting their systematic ID in. Multiple genes
- can be added by separating their names with spaces or line returns. The genes to
- transfer annotation to can be selected or de-selected. The toggle button above the gene
- list will toggle the selection.
-
- <p>
- On the right hand side are the qualifiers associated with the feature and any other
- features in the gene model. The qualifiers to be transferred are selected from this
- list. The '+' button expands to show the list of values associated with that qualifier
- from which those to be transferred can be selected.
-
- <p>
- Qualifiers on different features of the gene model that are selected will be transferred
- to the equivalent feature type in the genes they will be added to.
-
- <p>
- The default behavior is for qualifiers to be appended to any existing qualifiers.
- However if the 'Overwrite' check box is selected at the bottom of the tool then existing
- qualifiers of the same type will get deleted and it will add in the new qualifiers.
-
- <a NAME="WRITE"></a><h3>Writing To The Database</h3>
- When a feature or qualifier is changed, added or deleted the '<i>Commit</i>' button (on
- the top tool bar) changes colour to red. Changes in Artemis only get written back to the
- database when this button is clicked.
- <center><p><b><i>Commit Button</i></b><br>
- <img src="commit.gif" border="1"></center>
- <p>
- There is also an option under the '<i>File</i>' menu to '<i>Commit To
- Database</i>'. Note in ACT there is no commit button and the '<i>Commit To
- Database</i>' menu option is used to write back to the database.
- <p>
- If there is an error during the commit then Artemis will provide the option to
- force commit. This means it will commit what it can. Naturally this can be potentially
- problematic. Therefore, <b>committing back to the database frequently is encouraged</b>.
- Any errors are reported in the log viewer.
-
- <a NAME="COMMUNITY+ANNOTATION"></a><h3>Community Annotation</h3>
- Multiple users can launch Artemis and query the database. This has been stress
- tested and used in the malaria re-annotation exercise with 30+ Artemis clients
- connecting to the database.
- <p>
- Artemis records the time a features was last modified (<i>timelastmodified</i>). Before
- changing a feature it will check this time stamp against the database record of the
- <i>timelastmodified</i>.
- If the corresponding feature in the database has changed by another user it will
- ask whether to continue with the commit process.
-
- <a NAME="WRITING-SEQUENCE-FILES"></a><h3>Writing Out Sequence Files</h3>
- Artemis can write out EMBL and GFF files from the database. An option is given to
- optionally flatten the gene model to just a CDS feature. Also an option is given to ignore
- any obsolete features. For EMBL it uses mappings for conversion of the keys and qualifiers.
- These mappings are stored in the 'etc/key_mapping' and 'etc/qualifier_mapping'
- files.
- <p>
- A script (etc/writedb_entry) is also provided as a means of writing out multiple
- sequences from the database. The script takes the following options:
- <pre>
--h show help
--f [y|n] flatten the gene model, default is y
--i [y|n] ignore obsolete features, default is y
--s space separated list of sequences to read and write out
--o [EMBL|GFF] output format, default is EMBL
--a [y|n] for EMBL submission format change to n, default is y
- </pre>
-
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" dir="ltr" lang="en"><head>
-
-
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
- <meta name="KEYWORDS" content="Chado Data Storage">
-<meta name="robots" content="index,follow">
-<title>Chado Data Storage - SangerWiki</title>
-
-</head><body class="ns-0">
- <div id="globalWrapper">
- <div id="column-content">
- <div id="content">
- <a name="top" id="top"></a>
- <h1 class="firstHeading">Chado Data Storage</h1>
- <div id="bodyContent">
- <div id="contentSub"></div>
- <!-- start content -->
- <table id="toc" class="toc"><tbody><tr><td><div id="toctitle"><h2>Contents</h2> </div>
-<ul>
-<li class="toclevel-1"><a href="#Chado_Canonical_Gene"><span class="tocnumber">1</span> <span class="toctext">Chado Canonical Gene</span></a></li>
-<li class="toclevel-1"><a href="#Chado_Pseudogene"><span class="tocnumber">2</span> <span class="toctext">Chado Pseudogene</span></a></li>
-<li class="toclevel-1"><a href="#Gene_Model"><span class="tocnumber">3</span> <span class="toctext">Gene Model</span></a></li>
-<li class="toclevel-1"><a href="#Qualifier_Storage"><span class="tocnumber">4</span> <span class="toctext">Qualifier Storage</span></a>
-<ul>
-<li class="toclevel-2"><a href="#Note"><span class="tocnumber">4.1</span> <span class="toctext">Note</span></a></li>
-<li class="toclevel-2"><a href="#codon_start"><span class="tocnumber">4.2</span> <span class="toctext">codon_start</span></a></li>
-<li class="toclevel-2"><a href="#Similarity"><span class="tocnumber">4.3</span> <span class="toctext">Similarity</span></a></li>
-<li class="toclevel-2"><a href="#Controlled_Vocabulary_Qualifiers"><span class="tocnumber">4.4</span> <span class="toctext">Controlled Vocabulary Qualifiers</span></a>
-<ul>
-<li class="toclevel-3"><a href="#GO"><span class="tocnumber">4.4.1</span> <span class="toctext">GO</span></a></li>
-<li class="toclevel-3"><a href="#controlled_curation"><span class="tocnumber">4.4.2</span> <span class="toctext">controlled_curation</span></a></li>
-<li class="toclevel-3"><a href="#product"><span class="tocnumber">4.4.3</span> <span class="toctext">product</span></a></li>
-<li class="toclevel-3"><a href="#class_.28Riley_classification.29"><span class="tocnumber">4.4.4</span> <span class="toctext">class (Riley classification)</span></a></li>
-</ul>
-</li>
-<li class="toclevel-2"><a href="#Dbxref"><span class="tocnumber">4.5</span> <span class="toctext">Dbxref</span></a></li>
-<li class="toclevel-2"><a href="#EC_number"><span class="tocnumber">4.6</span> <span class="toctext">EC_number</span></a></li>
-<li class="toclevel-2"><a href="#literature"><span class="tocnumber">4.7</span> <span class="toctext">literature</span></a></li>
-<li class="toclevel-2"><a href="#Search_and_Results_files"><span class="tocnumber">4.8</span> <span class="toctext">Search and Results files</span></a>
-<ul>
-<li class="toclevel-3"><a href="#.2Fblast_file"><span class="tocnumber">4.8.1</span> <span class="toctext">/blast_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fblastn_file"><span class="tocnumber">4.8.2</span> <span class="toctext">/blastn_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fblastp.2Bgo_file"><span class="tocnumber">4.8.3</span> <span class="toctext">/blastp+go_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fblastp_file"><span class="tocnumber">4.8.4</span> <span class="toctext">/blastp_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fblastx_file"><span class="tocnumber">4.8.5</span> <span class="toctext">/blastx_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Ffasta_file"><span class="tocnumber">4.8.6</span> <span class="toctext">/fasta_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Ffastx_file"><span class="tocnumber">4.8.7</span> <span class="toctext">/fastx_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Ftblastn_file"><span class="tocnumber">4.8.8</span> <span class="toctext">/tblastn_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Ftblastx_file"><span class="tocnumber">4.8.9</span> <span class="toctext">/tblastx_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fclustalx_file"><span class="tocnumber">4.8.10</span> <span class="toctext">/clustalx_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fsigcleave_file"><span class="tocnumber">4.8.11</span> <span class="toctext">/sigcleave_file</span></a></li>
-<li class="toclevel-3"><a href="#.2Fpepstats_file"><span class="tocnumber">4.8.12</span> <span class="toctext">/pepstats_file</span></a></li>
-</ul>
-</li>
-<li class="toclevel-2"><a href="#Synonyms"><span class="tocnumber">4.9</span> <span class="toctext">Synonyms</span></a>
-<ul>
-<li class="toclevel-3"><a href="#.2Freserved_name"><span class="tocnumber">4.9.1</span> <span class="toctext">/reserved_name</span></a></li>
-<li class="toclevel-3"><a href="#.2Fsynonym"><span class="tocnumber">4.9.2</span> <span class="toctext">/synonym</span></a></li>
-<li class="toclevel-3"><a href="#.2Fprimary_name"><span class="tocnumber">4.9.3</span> <span class="toctext">/primary_name</span></a></li>
-<li class="toclevel-3"><a href="#.2Fprotein_name"><span class="tocnumber">4.9.4</span> <span class="toctext">/protein_name</span></a></li>
-<li class="toclevel-3"><a href="#.2Fsystematic_id"><span class="tocnumber">4.9.5</span> <span class="toctext">/systematic_id</span></a></li>
-<li class="toclevel-3"><a href="#.2Ftemporary_systematic_id"><span class="tocnumber">4.9.6</span> <span class="toctext">/temporary_systematic_id</span></a></li>
-</ul>
-</li>
-<li class="toclevel-2"><a href="#colour"><span class="tocnumber">4.10</span> <span class="toctext">colour</span></a></li>
-<li class="toclevel-2"><a href="#ortholog.2Fparalog.2Fcluster"><span class="tocnumber">4.11</span> <span class="toctext">ortholog/paralog/cluster</span></a></li>
-</ul>
-</li>
-</ul>
-</td></tr></tbody></table>
-<p><script type="text/javascript"> if (window.showTocToggle) { var tocShowText = "show"; var tocHideText = "hide"; showTocToggle(); } </script>
-</p>
-<a name="Chado_Canonical_Gene"></a><h2> Chado Canonical Gene </h2>
-<pre>gene
-|
-|- part_of mRNA
- |
- |---- part_of exon
- |
- |---- derives_from polypeptide
-</pre>
-<a name="Chado_Pseudogene"></a><h2> Chado Pseudogene </h2>
-<pre>pseudogene
-|
-|- part_of pseudogenic_transcript
- |
- |---- part_of pseudogenic_exon
- |
- |---- derives_from polypeptide
-</pre>
-<a name="Gene_Model"></a><h2> Gene Model </h2>
-<p><a href="Chado_gene_model.gif" class="image" title="Image:Chado_gene_model.gif"><img src="Chado_gene_model.gif" alt="Image:Chado_gene_model.gif" height="540" width="720"></a>
-</p>
-<a name="Qualifier_Storage"></a><h2> Qualifier Storage </h2>
-<a name="Note"></a><h3> Note </h3>
-<p>-stored as a FeatureProp with CvTerm = comment
-</p>
-<a name="codon_start"></a><h3> codon_start </h3>
-<p>This is loaded as phase in the FeatureLoc table.
-</p><p>phase = 0 => codon_start = 1;<br>
-phase = 1 => codon_start = 2;<br>
-phase = 2 => codon_start = 3
-</p>
-<a name="Similarity"></a><h3> Similarity </h3>
-<p><i>e.g.</i>: /similarity="fasta; SWALL:O85168
-(EMBL:AF047828);Pseudomonas syringae; syringomycin synthetase;
-syrE;length 9376 aa; id=31.93%; ungapped id=35.04%;E()=1.5e-105; ;
-6198 aa overlap; query 36-6020 aa; subject 2593-8452 aa"
-</p>
-<pre> analysis ------ fasta
- |
- |
- |
- analysisfeature ---- raw score (null), evalue, id
- |
- |
- | |---featureprop---ungapped id (35.04)
- | |
- Matchfeature ---|
- / | |
- / | |---featureprop---overlap (6198)
-rank=0 / |
-(srcfeature_id=product / |
-FeatureId) / |
-(subject 2593-8452)featureloc featureloc (query 36-6020) srcfeature_id=queryFeatureId rank=1
- | |
- | |
- featuredbxref | |
- (AF04782) | |
- \ | |
- \ | |
- \ | |
- \| |
-(dbxref=O85168) | |
-(seqlen=9376)feature feature (polypeptide if protein match | transcript if nucleotide match)
- /|\
- / | \
- / | \
- / | \
- / | \
- / | \
- / featureprop \
- featureprop | featureprop
- | | |
- | product |
- | (syringomycin s) |
- | |
- | |
- organism gene(syrE)
-(Pseudomonas syringae)
-
-</pre>
-<p>N.B. For now the match feature is entered as CvTerm = '<b>region'</b>.
-The Cv '<b>genedb_misc'</b> is used for Cvterms like 'ungapped id' found in /similarity.
-</p>
-<a name="Controlled_Vocabulary_Qualifiers"></a><h3> Controlled Vocabulary Qualifiers </h3>
-<p>These qualifiers are all FeatureCvTerm's.
-</p>
-<a name="GO"></a><h4> GO </h4>
-<p><br>
-/GO="aspect=;GOid=;term=;qualifer=;evidence='db_xref=;with=;date="
-</p>
-<p>GO annotation can be attached at different levels of the heirarchy.
-The GeneDB loader attaches it by default to the polypeptide as that
-seems to be the most typical case.
-</p>
-<p>Each GO entry has a CvTerm and a DbXRef associated with it. The GO
-term should be looked up by its DbXRef i.e. GO:123456, to get the
-correspontding CvTerm. A FeatureCvTerm links this CvTerm to the
-Feature. The FeatureCvTerm may well exist so needs to be looked up. The
-qualifier NOT is treated specially, as a field in FeatureCvTerm,
-becauses it reverses the meaning of the assignment, rather than adding
-more details as most qualifiers do. The FeatureCvTerm may have a number
-of associated FeatureCvTermProp's. This is general storage for the GO
-evidence code, extra qualifiers and the date of the assignment. (A hack
-for the evidence code would be possible, using a CvTerm to represent
-key and evidence code, but it wouldn't work for the date). One or more
-FeatureCvTermDbXRef's can be associated with the FeatureCvTerm which
-corresponds to the WITH/FROM column in GO. The dbxref value in this
-case correspond to publications, so the primary Pub is linked to the
-FeatureCvTerm.pub_id. One or more FeatureCvTermPub's can be associated
-with the FeatureCvTerm which corresponds to any ID's after the pipe
-symbol in the publication column.
-</p>
-<a name="controlled_curation"></a><h4> controlled_curation </h4>
-<p>/controlled_curation="term=;cv=; qualifier=;evidence=;db_xref=;residue=; attribution=;date="
-</p><p>Storage is similar to GO. The db_xref is stored either as a FeatureCvTermDbXref or a FeatureCvTermPub:
-</p>
-<ol><li> if the value is a PMID:12345 then it is stored in the pub
-table. a dummy dbxref is created with the 'accession' = 12345. a
-pubdbxref is created to link the pub with the dbxref.
-</li><li> if the value is other database like UNIPROT:23456 then it is
-stored in the dbxref table with accession=23456 and an entry is also
-created in the feature_cvterm_dbxref table to link the featurecvterm
-and the dbxref
-</li></ol>
-<a name="product"></a><h4> product </h4>
-<p>This is stored as a FeatureCvTerm with a CvTerm from the '<b>genedb_products'</b> Cv.
-</p>
-<a name="class_.28Riley_classification.29"></a><h4> class (Riley classification) </h4>
-<p><i>e.g.</i> /class=6.2.2
-</p>
-<p>
-These are linked to the Feature as below:
-
-</p><pre> Feature
- |
- FeatureCvTerm--name='anti sigma factor'
- |
- CvTerm
- |
- -----------
- | |
- RILEY--Cv DbXRef--accession=6.2.2
- |
- Db-name=RILEY
-</pre>
-
-<a name="Dbxref"></a><h3> Dbxref </h3>
-<p>- stored as a FeatureDbXRef
-</p>
-<a name="EC_number"></a><h3> EC_number </h3>
-<p>- stored as a FeatureProp
-</p>
-<a name="literature"></a><h3> literature </h3>
-<p>- stored as FeaturePub
-</p>
-<a name="Search_and_Results_files"></a><h3> Search and Results files </h3>
-<p>The following are stored as FeatureProp's:<br>
-</p>
-<a name=".2Fblast_file"></a><h4> /blast_file </h4>
-<a name=".2Fblastn_file"></a><h4> /blastn_file </h4>
-<a name=".2Fblastp.2Bgo_file"></a><h4> /blastp+go_file </h4>
-<a name=".2Fblastp_file"></a><h4> /blastp_file </h4>
-<a name=".2Fblastx_file"></a><h4> /blastx_file </h4>
-<a name=".2Ffasta_file"></a><h4> /fasta_file </h4>
-<a name=".2Ffastx_file"></a><h4> /fastx_file </h4>
-<a name=".2Ftblastn_file"></a><h4> /tblastn_file </h4>
-<a name=".2Ftblastx_file"></a><h4> /tblastx_file </h4>
-<a name=".2Fclustalx_file"></a><h4> /clustalx_file </h4>
-<a name=".2Fsigcleave_file"></a><h4> /sigcleave_file </h4>
-<a name=".2Fpepstats_file"></a><h4> /pepstats_file </h4>
-<a name="Synonyms"></a><h3> Synonyms </h3>
-<p>The following qualifiers are loaded in the Synonym table:<br>
-</p>
-<a name=".2Freserved_name"></a><h4> /reserved_name </h4>
-<a name=".2Fsynonym"></a><h4> /synonym </h4>
-<a name=".2Fprimary_name"></a><h4> /primary_name </h4>
-<a name=".2Fprotein_name"></a><h4> /protein_name </h4>
-<a name=".2Fsystematic_id"></a><h4> /systematic_id </h4>
-<a name=".2Ftemporary_systematic_id"></a><h4> /temporary_systematic_id </h4>
-<p>and these are linked to the Feature via FeatureSynonym's. These
-Synonym's are in the '<b>genedb_synonym_type'</b> Cv table.
-FeatureSynonym.is_current is used to store previous/obsolete
-synonyms.
-</p>
-<a name="colour"></a><h3> colour </h3>
-<p>Presumably a FeatureProp (at least for now). Additional qualifiers
-are being preposed status (containing information about functional
-annotation and whether the annotation is manual or automatic) and
-evidence. These are likely to be FeatureProp's.
-</p>
-<a name="ortholog.2Fparalog.2Fcluster"></a><h3> ortholog/paralog/cluster </h3>
-<p>Orthologue/paralogues cluster are stored in a similar way to <a href="#Similarity" title="">/similarity</a>.
-As input we have:
-<br>a) manually curated orthologues which simply list other genes'
-systematic ids and the relationship type
-<br>b) auto-generated clusters of genes which also have associated data like clustering method, cut-off/score etc.
-<br>However, they features are linked to each other by
-feature_relationship's (rather than featureloc which are used with
-/similarity). The feature_relationship's are given the type_id =
-'orthologous_to' or 'paralogous_to'. For manually curated
-ortholog/paralog data the analysisfeature and analysis are not required
-and are not added.
-</p>
-<pre>analysis
- |
- + analysisfeature
- |
- feature (type_id == protein_match)
- |
- +----+-------+------------+
- | | |
- | | |
-feature1 feature2 feature3
-gene gene gene
-
-</pre>
-<p>The bottom links are feature_relationships of SO type orthologous_to.
-</p>
-
- <div id="footer">
- </div>
- </div>
- </body></html>
diff --git a/docs/chado/writedb_entry.html b/docs/chado/writedb_entry.html
deleted file mode 100644
index dd6a9cb8fbf5e358b41419f4e4812f2e26315bbb..0000000000000000000000000000000000000000
--- a/docs/chado/writedb_entry.html
+++ /dev/null
@@ -1,137 +0,0 @@
-<style>
-
- body {
- background:#ffffff;
- color:#003366;
- font-family:sans-serif;
- }
-
- img.displayed {
- display: block;
- margin-left: auto;
- margin-right: auto
- }
-
- div.imageLegend {
- margin:auto;
- width:400px;
- text-align:center;
- color:#990000;
- font-style:italic;
- }
-
-
- code {
- background:#9999aa;
- color:white;
- margin:10px;
- padding:10px;
- font-weight:bold;
- display:block;
- white-space: pre;
- -webkit-border-radius: 10px;
- -moz-border-radius: 10px;
- }
-
-</style>
-
-<h3>writedb_entry - exports EMBL or GFF3 files from Chado.</h3>
-
-<h3>Synopsys</h3>
-<P>
-writedb_entry is a wrapper script around Artemis's ReadAndWrite entry functions, which allows export to EMBL and GFF3 formats. It can be run in 3 ways.
-<P></P>
-The default method is the 'swing' method (because that's the original behaviour), which assumes that you are running it either on your own machine or on a server with X11 forwarding setup. Any errors or login prompts will popup in a graphical user interface as windows. In this mode, if it is not on your machine or no X11 is available, then any attempts to prompt will result in exceptions.
-<P></P>
-The 'console' mode is for running interactively on the shell without the need for a graphical user interface. All user-prompting (like password entry) is done inside the shell. Useful for one-offs where there is no X11 forwarding.
-<P></P>
-The 'script' mode is for batch runs where you don't want any user prompting. Passwords must be supplied as a command line parameter if needed in this case.
-</P>
-<h3>Command line parameters</h3>
-
-<dl>
- <dt>-f</dt> <dd>[y|n] flatten the gene model, default is y</dd>
-
- <dt>-i</dt> <dd>[y|n] ignore obsolete features, default is y</dd>
-
- <dt>-s</dt> <dd>space separated list of sequences to read and write out</dd>
-
- <dt>-o</dt> <dd>[EMBL|GFF] output format, default is EMBL</dd>
-
- <dt>-a</dt> <dd>[y|n] for EMBL submission format change to n, default is y</dd>
-
- <dt>-pp</dt> <dd>[y|n] read polypeptide domain features, default is n</dd>
-
- <dt>-c</dt> <dd>the URL for your Chado database e.g. db.genedb.org:5432/snapshot?genedb_ro (you can also do this by using the -Dchado=... method, but this -c parameter will override that) </dd>
-
- <dt>-u</dt> <dd>[swing|console|script] the UI mode : run in swing (with popup dialog boxes) mode, run in console mode (choices entered in the console window), or in script mode (all choices default to continue, all parameters passed on command line) </dd>
-
- <dt>-p</dt> <dd>the password for connecting to the Chado database (this is required in script mode, where passwords can not be passed interactively)</dd>
-
- <dt>-fp</dt> <dd>the file path (the folder you want to save the files in)</dd>
-
-</dl>
-<h3>Examples</h3>
-
-
-<h4>1. Using in swing mode. </h4>
-
-All prompting would then happen via graphical dialog boxes. In this example I am running this locally on my desktop machine.
-
-<CODE>$ /Volumes/us/data/gv1/workspace/artemis/etc/writedb_entry -c "db.genedb.org:5432/snapshot?genedb_ro" -o GFF -s Tcruzi_999
-
-read :: Tcruzi_999 write :: Tcruzi_999.gff
-reading options from "/Users/gv1/.artemis_options"
-done
-</CODE>
-
-<img class="displayed" src="prompt1.png">
-<div class="imageLegend">A prompt for login details.</div>
-<img class="displayed" src="prompt2.png">
-<div class="imageLegend">A prompt detailing a problem.</div>
-
-
-
-
-
-
-<h4>2. Using interactively in console mode : </h4>
-
-All prompting would then happen on the console. In this example I am running this on a server.
-
-<CODE>$ writedb_entry -c "db.genedb.org:5432/snapshot?genedb_ro" -o GFF -u console -s Tcruzi_999
-
-read :: Tcruzi_999 write :: Tcruzi_999.gff
-Enter Password:
-Destination format can't handle all keys/qualifiers - continue?
-region can't have isObsolete as a qualifier(y/n): y
-done
-
-</CODE>
-
-
-
-
-
-
-
-<h4>3. Using in script mode : </h4>
-
-In these examples I am running them on a server. Note that there is no password needed as it's going to the public snapshot.
-
-<CODE>$ writedb_entry -c "db.genedb.org:5432/snapshot?genedb_ro" -o GFF -u script -s Tcruzi_999
-
-read :: Tcruzi_999 write :: Tcruzi_999.gff
-Desti
-</CODE>
-
-If there was a password needed, you would have to enter it as follows.
-
-<CODE>$ writedb_entry -c "db.genedb.org:5432/snapshot?genedb_ro" -o GFF -u script -p mypass -s Tcruzi_999
-
-read :: Tcruzi_999 write :: Tcruzi_999.gff
-Destination format can't handle all keys/qualifiers - continue? : region can't have isObsolete as a qualifier : y
-done
-
-</CODE>
-
diff --git a/pom.xml b/pom.xml
index 93ab61477623fc7a67a12ad94866d2f8fc527b73..a05d8f1a0ddfc625ce706bf939f1e3aa73404338 100644
--- a/pom.xml
+++ b/pom.xml
@@ -45,7 +45,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<licenses>
<license>
<name>The GNU General Public License, Version 3, June 2007</name>
- <url>https://github.com/sanger-pathogens/Artemis/blob/master/LICENSE</url>
+ <url>https://raw.githubusercontent.com/sanger-pathogens/Artemis/master/LICENSE</url>
</license>
</licenses>
@@ -92,6 +92,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<java.source.version>1.8</java.source.version>
<java.target.version>1.8</java.target.version>
<java.javadoc.url>https://docs.oracle.com/javase/8/docs/api/</java.javadoc.url>
+ <osx.jdk.path>${env.JAVA_HOME}/../..</osx.jdk.path>
<!-- Evosuite properties-->
<targetFolder>src/test/evosuite</targetFolder>
@@ -99,7 +100,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<evosuite.plugin.version>1.0.6</evosuite.plugin.version>
<!-- Assembly folders -->
- <bioconda.assembly.folder>artemis</bioconda.assembly.folder>
<windows.assembly.folder>artemis</windows.assembly.folder>
<unix.assembly.folder>artemis</unix.assembly.folder>
<osx.assembly.folder>artemis</osx.assembly.folder>
@@ -108,25 +108,31 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<release.artifact.folder>${project.build.directory}/release-artifacts</release.artifact.folder>
<windows.release.folder>${release.artifact.folder}/windows-release</windows.release.folder>
<osx.app.folder>${release.artifact.folder}/mac-osx-release</osx.app.folder>
+ <osx.app.chado.folder>${release.artifact.folder}/mac-osx-chado-release</osx.app.chado.folder>
<unix.release.folder>${release.artifact.folder}/unix-release</unix.release.folder>
- <bioconda.release.folder>${release.artifact.folder}/bioconda-release</bioconda.release.folder>
<!-- Release file names -->
- <bioconda.release.filename>artemis-bioconda-release-${project.version}</bioconda.release.filename>
<unix.release.filename>artemis-unix-release-${project.version}</unix.release.filename>
<windows.release.filename>artemis-windows-release-${project.version}</windows.release.filename>
<osx.release.filename>artemis-macosx-release-${project.version}</osx.release.filename>
+ <osx.chado.release.filename>artemis-macosx-chado-release-${project.version}</osx.chado.release.filename>
+
+ <!-- Mac OS application JVM options -->
+ <postgres.command.line.arg>-Djdbc.drivers=org.postgresql.Driver</postgres.command.line.arg>
+ <maxheap.command.line.arg>-mx2g</maxheap.command.line.arg>
+ <initialheap.command.line.arg>-ms128m</initialheap.command.line.arg>
+ <noverify.command.line.arg>-noverify</noverify.command.line.arg>
+ <unixenv.command.line.arg>-Dartemis.environment=UNIX</unixenv.command.line.arg>
+ <macosx.menuname.command.line.arg>-Dcom.apple.mrj.application.apple.menu.about.name</macosx.menuname.command.line.arg>
+ <macosx.dock.command.line.arg>-Xdock:name</macosx.dock.command.line.arg>
+ <chado.command.line.arg>-Dchado="localhost:5432/databasename?username"</chado.command.line.arg>
+ <ibatis.command.line.arg>-Dibatis</ibatis.command.line.arg>
+ <sangeroptions.command.line.arg>-Dsanger_options=yes</sangeroptions.command.line.arg>
+ <j2ssh.command.line.arg>-Dj2ssh</j2ssh.command.line.arg>
<!-- Surefire unit test plugin arguments -->
- <surefireArgLine>-Xmx4g -noverify -Djdbc.drivers=org.postgresql.Driver -Duse_separate_classloader=false -DEMBOSS_ROOT=${emboss.installation.root}</surefireArgLine>
-
- <!-- Application JVM options -->
- <jvm.options.base>-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX -mx2g -ms128m -noverify</jvm.options.base>
- <jvm.options.artemis>${jvm.options.base} -Dcom.apple.mrj.application.apple.menu.about.name=${artemis.application.name} -Dapple.laf.useScreenMenuBar=true -Xdock:name=${artemis.application.name}</jvm.options.artemis>
- <jvm.options.act>${jvm.options.base} -Dcom.apple.mrj.application.apple.menu.about.name=${act.application.name} -Dapple.laf.useScreenMenuBar=true -Xdock:name=${act.application.name}</jvm.options.act>
- <jvm.options.dnaplotter>${jvm.options.base} -Dcom.apple.mrj.application.apple.menu.about.name=${dnaplotter.application.name} -Dapple.laf.useScreenMenuBar=true -Xdock:name=${dnaplotter.application.name}</jvm.options.dnaplotter>
- <jvm.options.bamview>${jvm.options.base} -Dcom.apple.mrj.application.apple.menu.about.name=${bamview.application.name} -Dapple.laf.useScreenMenuBar=false -Xdock:name=${bamview.application.name}</jvm.options.bamview>
-
+ <surefireArgLine>-Xmx4g ${noverify.command.line.arg} ${postgres.command.line.arg} -Duse_separate_classloader=false -DEMBOSS_ROOT=${emboss.installation.root}</surefireArgLine>
+
<docs.folder>${project.basedir}/docs</docs.folder>
<docs.output.folder>${project.build.directory}/docs</docs.output.folder>
@@ -134,7 +140,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<default.file.excludes>**/log4j*.xml META-INF/* **/.DS_Store **/._*</default.file.excludes>
<!-- Etc files to exclude from the build. -->
- <etc.file.excludes>*.html *.seq *.fasta *.embl *.tab *.crunch *.genbank</etc.file.excludes>
+ <etc.file.excludes>*.seq *.fasta *.embl *.tab *.crunch *.genbank</etc.file.excludes>
<artemis.icons.path>${project.basedir}/icons</artemis.icons.path>
@@ -249,7 +255,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
- <version>42.2.1</version>
+ <version>42.2.5</version>
</dependency>
<!-- Using latest version gives compilation errors! -->
@@ -262,7 +268,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<!-- Start of Picard jars -->
<!-- https://mvnrepository.com/artifact/com.github.broadinstitute/picard -->
- <!-- Latest as of 24th Set 2018 -->
+ <!-- Latest as of 24th Sept 2018 -->
<!-- It contains two htsjdk fixes for CRAM index caching and the query mate issue -->
<dependency>
<groupId>com.github.broadinstitute</groupId>
@@ -348,7 +354,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</executions>
</plugin>
- <!-- ====================== Read project build properties ======================= -->
+ <!-- ====================== Read signing related properties ======================= -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
@@ -362,6 +368,8 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<goal>read-project-properties</goal>
</goals>
<configuration>
+ <!-- Build will not fail if properties file is not found, but signing will fail -->
+ <quiet>true</quiet>
<files>
<file>maven.properties</file>
</files>
@@ -408,8 +416,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<generatePom>true</generatePom>
</configuration>
</execution>
-
- <!-- NEEDS UPGRADE.... -->
<execution>
<id>install-j2ssh-core-jar</id>
<phase>validate</phase>
@@ -425,7 +431,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<generatePom>true</generatePom>
</configuration>
</execution>
-
<execution>
<id>install-ibatis-jar</id>
<phase>validate</phase>
@@ -476,6 +481,25 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</configuration>
</plugin>
+ <!-- ============================== Jar customisation ===================================== -->
+
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>3.1.0</version>
+ <configuration>
+ <archive>
+ <manifest>
+ <addClasspath>false</addClasspath>
+ </manifest>
+ <manifestEntries>
+ <Permissions>all-permissions</Permissions>
+ <Codebase>*</Codebase>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+
<!-- ============================== Copy resources to build folder ======================== -->
<plugin>
@@ -532,7 +556,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</configuration>
</execution>
<!-- Copy non-maven legacy jars to build area for inclusion in assembly -->
- <execution>
+ <!-- execution>
<id>copy-old-jars</id>
<phase>process-test-resources</phase>
<goals>
@@ -546,7 +570,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</resource>
</resources>
</configuration>
- </execution>
+ </execution-->
<execution>
<id>copy-icons-to-target-folder</id>
<phase>package</phase>
@@ -1069,9 +1093,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</plugin>
-
-
-
<!-- ========================== Create release zips ============================ -->
<plugin>
@@ -1079,21 +1100,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<executions>
- <execution>
- <id>create-bioconda-release</id>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- <configuration>
- <appendAssemblyId>false</appendAssemblyId>
- <outputDirectory>${bioconda.release.folder}</outputDirectory>
- <descriptors>
- <descriptor>src/assembly/bioconda-release-assembly.xml</descriptor>
- </descriptors>
- <finalName>${bioconda.release.filename}</finalName>
- </configuration>
- </execution>
<execution>
<id>create-unix-release</id>
<phase>package</phase>
@@ -1227,6 +1233,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<failOnError>false</failOnError>
<quiet>true</quiet>
<excludePackageNames>org.*</excludePackageNames>
+ <excludes>**/*Test.java, **/*_scaffolding*.java</excludes>
</configuration>
<reportSets>
<reportSet>
@@ -1242,15 +1249,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</reporting>
- <!-- Site deployment -->
- <!-- distributionManagement>
- <site>
- <id>site.deployments</id>
- <name>Site deployments</name>
- <url></url>
- </site>
- </distributionManagement -->
-
<!-- ========================== Profile section =================================-->
@@ -1274,38 +1272,20 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</properties>
</profile>
- <!-- dev-evo profile that will also run all evosuite tests (which takes a long time) -->
- <!-- profile>
- <id>dev-evo</id>
- <activation>
- <activeByDefault>false</activeByDefault>
- </activation>
- <properties>
- <skip.tests>false</skip.tests>
- <evosuite.exclude.filter></evosuite.exclude.filter>
- <jarsigner.skip>true</jarsigner.skip>
- <skip.artifact.creation>true</skip.artifact.creation>
- <skip.coverage.reporting>false</skip.coverage.reporting>
- <skip.javadoc>true</skip.javadoc>
-
- <build.profile.id>dev-evo</build.profile.id>
- </properties>
- </profile -->
-
<profile>
- <id>site</id>
+ <id>release</id>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<skip.tests>false</skip.tests>
- <evosuite.exclude.filter></evosuite.exclude.filter>
+ <evosuite.exclude.filter>**/*_ESTest*</evosuite.exclude.filter>
<jarsigner.skip>false</jarsigner.skip>
<skip.artifact.creation>false</skip.artifact.creation>
<skip.coverage.reporting>false</skip.coverage.reporting>
<skip.javadoc>false</skip.javadoc>
- <build.profile.id>site</build.profile.id>
+ <build.profile.id>release</build.profile.id>
</properties>
<build>
<plugins>
@@ -1333,11 +1313,20 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${artemis.application.name}</bundleName>
- <jrePath>${java.jdk.home}</jrePath>
+ <jrePath>${osx.jdk.path}</jrePath>
<mainClass>${artemis.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/artemis.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
- <jvmOptions>${jvm.options.artemis}</jvmOptions>
+ <jvmOptions>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${artemis.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${artemis.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
@@ -1360,11 +1349,20 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${act.application.name}</bundleName>
- <jrePath>${java.jdk.home}</jrePath>
+ <jrePath>${osx.jdk.path}</jrePath>
<mainClass>${act.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/act.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
- <jvmOptions>${jvm.options.act}</jvmOptions>
+ <jvmOptions>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${act.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${act.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
@@ -1387,11 +1385,20 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${dnaplotter.application.name}</bundleName>
- <jrePath>${java.jdk.home}</jrePath>
+ <jrePath>${osx.jdk.path}</jrePath>
<mainClass>${dnaplotter.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/dnaplotter.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
- <jvmOptions>${jvm.options.dnaplotter}</jvmOptions>
+ <jvmOptions>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${dnaplotter.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${dnaplotter.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
@@ -1416,11 +1423,175 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<generateDiskImageFile>true</generateDiskImageFile>
<diskImageFile>${osx.app.folder}/${osx.release.filename}.dmg</diskImageFile>
<bundleName>${bamview.application.name}</bundleName>
- <jrePath>${java.jdk.home}</jrePath>
+ <jrePath>${osx.jdk.path}</jrePath>
+ <mainClass>${bamview.main.class}</mainClass>
+ <iconFile>${project.build.directory}/icons/bamview.icns</iconFile>
+ <jvmVersion>${java.target.version}</jvmVersion>
+ <jvmOptions>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${bamview.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${bamview.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
+ <additionalBundledClasspathResources>
+ <fileSet>
+ <directory>${project.build.directory}/icons</directory>
+ <includes>
+ <include>Readme.txt</include>
+ </includes>
+ </fileSet>
+ </additionalBundledClasspathResources>
+ </configuration>
+ </execution>
+
+ <!-- Package CHADO version of toolkit -->
+
+ <execution>
+ <id>create-artemis-osx-app-CHADO</id>
+ <phase>package</phase>
+ <goals>
+ <goal>bundle</goal>
+ </goals>
+ <configuration>
+ <skip>${skip.artifact.creation}</skip>
+ <version>${project.version}</version>
+ <buildDirectory>${osx.app.chado.folder}</buildDirectory>
+ <generateDiskImageFile>false</generateDiskImageFile>
+ <bundleName>${artemis.application.name} (CHADO)</bundleName>
+ <jrePath>${osx.jdk.path}</jrePath>
+ <mainClass>${artemis.main.class}</mainClass>
+ <iconFile>${project.build.directory}/icons/artemis.icns</iconFile>
+ <jvmVersion>${java.target.version}</jvmVersion>
+ <jvmOptions>
+ <jvmOption>${postgres.command.line.arg}</jvmOption>
+ <jvmOption>${chado.command.line.arg}</jvmOption>
+ <jvmOption>${ibatis.command.line.arg}</jvmOption>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${artemis.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${artemis.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
+ <additionalBundledClasspathResources>
+ <fileSet>
+ <directory>${project.build.directory}/icons</directory>
+ <includes>
+ <include>Readme.txt</include>
+ </includes>
+ </fileSet>
+ </additionalBundledClasspathResources>
+ </configuration>
+ </execution>
+ <execution>
+ <id>create-act-osx-app-CHADO</id>
+ <phase>package</phase>
+ <goals>
+ <goal>bundle</goal>
+ </goals>
+ <configuration>
+ <skip>false</skip>
+ <version>${project.version}</version>
+ <buildDirectory>${osx.app.chado.folder}</buildDirectory>
+ <generateDiskImageFile>false</generateDiskImageFile>
+ <bundleName>${act.application.name} (CHADO)</bundleName>
+ <jrePath>${osx.jdk.path}</jrePath>
+ <mainClass>${act.main.class}</mainClass>
+ <iconFile>${project.build.directory}/icons/act.icns</iconFile>
+ <jvmVersion>${java.target.version}</jvmVersion>
+ <jvmOptions>
+ <jvmOption>${postgres.command.line.arg}</jvmOption>
+ <jvmOption>${chado.command.line.arg}</jvmOption>
+ <jvmOption>${ibatis.command.line.arg}</jvmOption>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${act.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${act.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
+ <additionalBundledClasspathResources>
+ <fileSet>
+ <directory>${project.build.directory}/icons</directory>
+ <includes>
+ <include>Readme.txt</include>
+ </includes>
+ </fileSet>
+ </additionalBundledClasspathResources>
+ </configuration>
+ </execution>
+ <execution>
+ <id>create-dnaplotter-osx-app-CHADO</id>
+ <phase>package</phase>
+ <goals>
+ <goal>bundle</goal>
+ </goals>
+ <configuration>
+ <skip>false</skip>
+ <version>${project.version}</version>
+ <buildDirectory>${osx.app.chado.folder}</buildDirectory>
+ <generateDiskImageFile>false</generateDiskImageFile>
+ <bundleName>${dnaplotter.application.name}</bundleName>
+ <jrePath>${osx.jdk.path}</jrePath>
+ <mainClass>${dnaplotter.main.class}</mainClass>
+ <iconFile>${project.build.directory}/icons/dnaplotter.icns</iconFile>
+ <jvmVersion>${java.target.version}</jvmVersion>
+ <jvmOptions>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${dnaplotter.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${dnaplotter.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
+ <additionalBundledClasspathResources>
+ <fileSet>
+ <directory>${project.build.directory}/icons</directory>
+ <includes>
+ <include>Readme.txt</include>
+ </includes>
+ </fileSet>
+ </additionalBundledClasspathResources>
+ </configuration>
+ </execution>
+ <!-- The last execution also creates the disk image file... -->
+ <execution>
+ <id>create-bamview-osx-app-CHADO</id>
+ <phase>package</phase>
+ <goals>
+ <goal>bundle</goal>
+ </goals>
+ <configuration>
+ <skip>false</skip>
+ <version>${project.version}</version>
+ <buildDirectory>${osx.app.chado.folder}</buildDirectory>
+ <generateDiskImageFile>true</generateDiskImageFile>
+ <diskImageFile>${osx.app.chado.folder}/${osx.chado.release.filename}.dmg</diskImageFile>
+ <bundleName>${bamview.application.name}</bundleName>
+ <jrePath>${osx.jdk.path}</jrePath>
<mainClass>${bamview.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/bamview.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
- <jvmOptions>${jvm.options.bamview}</jvmOptions>
+ <jvmOptions>
+ <jvmOption>${maxheap.command.line.arg}</jvmOption>
+ <jvmOption>${initialheap.command.line.arg}</jvmOption>
+ <jvmOption>${noverify.command.line.arg}</jvmOption>
+ <jvmOption>${unixenv.command.line.arg}</jvmOption>
+ <jvmOption>${macosx.menuname.command.line.arg}=${bamview.application.name}</jvmOption>
+ <jvmOption>${macosx.dock.command.line.arg}=${bamview.application.name}</jvmOption>
+ <jvmOption>${sangeroptions.command.line.arg}</jvmOption>
+ <jvmOption>${j2ssh.command.line.arg}</jvmOption>
+ </jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
@@ -1432,8 +1603,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
</configuration>
</execution>
</executions>
- </plugin>
-
+ </plugin>
</plugins>
</build>
</profile>
diff --git a/src/assembly/bioconda-release-assembly.xml b/src/assembly/bioconda-release-assembly.xml
deleted file mode 100644
index 2a8c58d53a861755c3b339a39ea3d3a9e858f395..0000000000000000000000000000000000000000
--- a/src/assembly/bioconda-release-assembly.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
- http://maven.apache.org/xsd/assembly-1.1.2.xsd">
-
- <!-- Assembles a simple release zip with jars and scripts -->
- <id>assemble-bioconda-release</id>
- <formats>
- <format>zip</format>
- </formats>
- <includeBaseDirectory>false</includeBaseDirectory>
-
- <fileSets>
- <fileSet>
- <directory>target/jars</directory>
- <outputDirectory>${bioconda.assembly.folder}</outputDirectory>
- <includes>
- <include>*.jar</include>
- </includes>
- </fileSet>
- <fileSet>
- <outputDirectory>${bioconda.assembly.folder}</outputDirectory>
- <includes>
- <include>AUTHORS</include>
- <include>LICENSE</include>
- <include>README*</include>
- </includes>
- </fileSet>
- <fileSet>
- <outputDirectory>${bioconda.assembly.folder}</outputDirectory>
- <includes>
- <include>art</include>
- <include>act</include>
- <include>dnaplotter</include>
- <include>bamview</include>
- <include>setenv</include>
- </includes>
- <fileMode>0755</fileMode>
- <lineEnding>unix</lineEnding>
- </fileSet>
- </fileSets>
-</assembly>
-
diff --git a/src/assembly/unix-release-assembly.xml b/src/assembly/unix-release-assembly.xml
index d749e1e12a737448aef5d6a49c4dff9cc1404c5a..543f5a682d110de99e4c5497b98deba9b06ce137 100644
--- a/src/assembly/unix-release-assembly.xml
+++ b/src/assembly/unix-release-assembly.xml
@@ -8,6 +8,7 @@
<id>assemble-unix-release</id>
<formats>
<format>tar.gz</format>
+ <format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
@@ -20,14 +21,6 @@
<include>*.jar</include>
</includes>
</fileSet>
- <fileSet>
- <directory>etc</directory>
- <outputDirectory>${unix.assembly.folder}/etc</outputDirectory>
- <includes>
- <include>*</include>
- </includes>
- <lineEnding>unix</lineEnding>
- </fileSet>
<fileSet>
<outputDirectory>${unix.assembly.folder}</outputDirectory>
<includes>
diff --git a/src/assembly/windows-release-assembly.xml b/src/assembly/windows-release-assembly.xml
index 76f1c7b1c1e4ccb3cb849286c32ca36dd847b3b1..3b992a81ce513fbbcc2f6be6458e72db04e3177b 100644
--- a/src/assembly/windows-release-assembly.xml
+++ b/src/assembly/windows-release-assembly.xml
@@ -20,6 +20,14 @@
<include>*.jar</include>
</includes>
</fileSet>
+ <fileSet>
+ <outputDirectory>${windows.assembly.folder}</outputDirectory>
+ <includes>
+ <include>AUTHORS</include>
+ <include>LICENSE</include>
+ <include>README*</include>
+ </includes>
+ </fileSet>
</fileSets>
</assembly>