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Commit 7216313a authored by tcarver's avatar tcarver
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Merge pull request #198 from tcarver/master

misc
parents 1777fcee b619c31a
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Installation instructions for UNIX
==================================
1. change to /some/directory
2. uncompress and untar the artemis_compiled.tar.gz file
On UNIX the command is: gzip -d < artemis_compiled.tar.gz | tar xf -
On UNIX the command is: tar xzvf artemis_compiled.tar.gz
This will create a "artemis" directory containing all the java classes. On
Unix the easiest way to run the program is to run the script called art in the
......@@ -18,7 +17,8 @@ menus. From the File menu you can open a flat file containing an
entry. If it reads the entry successfully a new window will open,
which shows the sequence and features for the entry.
====================================================================
Download and Install from GitHub
================================
Installation instructions for GitHub download
......@@ -31,3 +31,41 @@ Installation instructions for GitHub download
./art
or ACT:
./act
Makefile targets
================
make - compile code
make jar - create Artemis (jar_build/artemis.jar) and ACT
(jar_build/act.jar) jar files.
make dist - create a tar ball of the Artemis/ACT distribution
Creating signed jar files for Artemis/ACT Java Web Start launch
===============================================================
Use 'make jar' to create jar_build/artemis.jar. See the following pages
for a description of deploying and signing jar files:
http://java.sun.com/docs/books/tutorial/deployment/webstart/deploying.html
http://java.sun.com/docs/books/tutorial/deployment/jar/signing.html
Use the Java keytool to generate a keystore (e.g. artemisstore below) file:
keytool -genkey -alias signFiles -dname "CN=$NAME, \
OU=$ORGU, O=$ORG, L=$LOC, S=$STATE, C=$CODE" \
-keypass $KEYPASS -storepass $STOREPASS -keystore artemisstore -validity $VALID
The following can be used to view the key store and list entry details:
keytool -list -v -keystore artemisstore
Then use the following to create a signed jar to use in the JNLP file:
jarsigner -keystore artemisstore -storepass $STOREPASS -keypass $KEYPASS \
-signedjar sartemis.jar artemis.jar signFiles
Running the test suite
======================
cd test
ant -f build-test.xml
Artemis Release 16.0.8
ACT Release 13.0.8
Artemis Release 16.0.9
ACT Release 13.0.9
DNAPlotter Release 1.11
BamView 1.2.13
\ No newline at end of file
gff2embl 0 → 100755
#!/bin/sh -
# Command line utility for coverting GFF to EMBL
PRG=$0
progname=`basename $0`
ARTEMIS_HOME=`dirname "$PRG"`/.
CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH
# j2ssh jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/j2ssh/commons-logging.jar:$ARTEMIS_HOME/lib/j2ssh/j2ssh-core.jar:$ARTEMIS_HOME/lib/j2ssh/
# iBatis jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar
export CLASSPATH
# batik jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/batik/batik-awt-util.jar:$ARTEMIS_HOME/lib/batik/batik-dom.jar:$ARTEMIS_HOME/lib/batik/batik-ext.jar:$ARTEMIS_HOME/lib/batik/batik-svggen.jar:$ARTEMIS_HOME/lib/batik/batik-util.jar:$ARTEMIS_HOME/lib/batik/batik-xml.jar
# picard jars
CLASSPATH=$ARTEMIS_HOME/lib/picard/sam.jar:$ARTEMIS_HOME/lib/picard/picard.jar:$ARTEMIS_HOME/lib/commons-net-2.2.jar:$CLASSPATH
CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
export CLASSPATH
if [ $# = 0 ]
then
:
else
if [ "$1" = "-h" -o "$1" = "--help" -o "$1" = "-help" ]
then
cat <<EOF
SYNOPSIS
gff2embl
USAGE
$0 [options] <SEQUENCE_FILE>
OPTIONS
SEQUENCE_FILE A GFF3 file
-s FILE space separated list of GFF files to read and write out
-o OUTPUT_DIR output directory
-f [y/n] flatten the gene model, default is y
-z gzip output, default is y
-a [y|n] for EMBL submission format change to n, default is y
EXAMPLES
% -s /Users/tjc/test.gff -o /Users/tjc
HOMEPAGE
http://www.sanger.ac.uk/resources/software/artemis/
EOF
exit 0
fi
fi
ARTEMIS_PROPERTIES="-Dartemis.environment=UNIX"
# Allow URLs to work from behind firewalls
if [ "$http_proxy" = "" ]
then
http_proxy=$HTTP_PROXY
fi
if [ "$http_proxy" = "" ]
then
http_proxy=$HTTP_proxy
fi
if [ "$http_proxy" != "" ]
then
ARTEMIS_PROPERTIES="$ARTEMIS_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
fi
# "-mx500m" sets the maximum amount of memory that Artemis can use. This may
# need to be increased when dealing with large files
MEM="-mx500m -ms20m"
if [ "$JVM_FLAGS" = "" ]
then
FLAGS="$MEM -noverify"
else
FLAGS="$MEM -noverify $JVM_FLAGS"
fi
FLAGS=$FAST_FLAG$FLAGS
if [ "$JAVA_VM" = "" ]
then
if [ "$DEBUG" = yes ]
then
JAVA=java_g
else
JAVA=java
fi
else
JAVA=$JAVA_VM
fi
PLATTMP=`uname`
if [ "$PLATTMP" = "Darwin" ]
then
FLAGS="$FLAGS -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Circular Plot"
fi
$JAVA $MEM uk.ac.sanger.artemis.io.GffToEMBL $*
......@@ -31,6 +31,8 @@ import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.File;
import java.io.IOException;
import javax.swing.JOptionPane;
/**
* This class contains the method makeDocumentEntry (), which creates a
......@@ -79,8 +81,19 @@ abstract public class DocumentEntryFactory
document.getInputStream() instanceof net.sf.samtools.util.BlockCompressedInputStream)
{
if(IndexedGFFDocumentEntry.isIndexed( ((File)document.getLocation()) ))
{
Object[] possibleValues = { "Use index", "Ignore index" };
int sel = JOptionPane.showOptionDialog(null,
"Use the GFF index file (to increase the performance)\n"+
"or concatenate the sequences together?",
"Indexed GFF",
JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
null, possibleValues, possibleValues[0]);
if(sel == 0)
return new IndexedGFFDocumentEntry(document);
}
}
final LinePushBackReader document_reader =
document.getLinePushBackReader();
......
......@@ -224,7 +224,7 @@ class GffToEMBL
(args == null || args.length < 1))
{
System.out.println("-h\tshow help");
System.out.println("-s\tspace separated list of sequences to read and write out");
System.out.println("-s\tspace separated list of GFF files to read and write out");
System.out.println("-o\toutput directory");
System.out.println("-f\t[y|n] flatten the gene model, default is y");
System.out.println("-z\t[y|n] gzip output, default is y");
......
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