From 2e18efdfdc8dadf20680e0cd4633aa40b3efe8a1 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 6 Jan 2011 11:15:53 +0000
Subject: [PATCH] update
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15316 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
docs/act_file_menu.sgml | 2 +-
docs/act_start_chapter.sgml | 11 ++++++++---
docs/file_menu.sgml | 2 +-
docs/next_gen.sgml | 2 +-
4 files changed, 11 insertions(+), 6 deletions(-)
diff --git a/docs/act_file_menu.sgml b/docs/act_file_menu.sgml
index 6a5b24de7..012921145 100644
--- a/docs/act_file_menu.sgml
+++ b/docs/act_file_menu.sgml
@@ -43,7 +43,7 @@ URL="http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html"><COMMAND>MSPcrun
The output of <ULINK URL="http://www.ncbi.nlm.nih.gov/BLAST/">blastall</ULINK>
version 2.2.2 or better. <COMMAND>blastall</COMMAND> must be run with the
<COMMAND>-m 8</COMMAND> flag which generates one line of information per HSP.
-Note that currently &prog; displays each Blast HSP is a separate feature
+Note that currently &prog; displays each Blast HSP as a separate feature
rather than displaying each BLAST hit as a feature.
</PARA>
</LISTITEM>
diff --git a/docs/act_start_chapter.sgml b/docs/act_start_chapter.sgml
index c628051ec..484fc5115 100644
--- a/docs/act_start_chapter.sgml
+++ b/docs/act_start_chapter.sgml
@@ -15,7 +15,12 @@ Before running &prog; you will need to obtain a comparison file.
</ULINK> version 2.2.2 or better</TITLE>
<PARA>
The <COMMAND>blastall</COMMAND> command must be run with the <COMMAND>-m
-8</COMMAND> flag which generates one line of information per HSP.
+8</COMMAND> flag which generates one line of information per HSP. If
+<ULINK URL="http://blast.ncbi.nlm.nih.gov/">BLAST+</ULINK>
+is used then the legacy_blast.pl PERL script (bundled along with the BLAST+ applications)
+can be used to generate the tabular format or run it with the <COMMAND>-outfmt 6</COMMAND> flag.
+For more details see the <ULINK URL=
+"ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/user_manual.pdf">BLAST+ manual</ULINK>.
</PARA>
</FORMALPARA>
</LISTITEM>
@@ -33,7 +38,7 @@ which is part of the blast distribution.
<FORMALPARA>
<TITLE>MSPcrunch output</TITLE>
<PARA>
-<ULINK URL="http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html"
+<ULINK URL="http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/"
TYPE="external">MSPcrunch</ULINK> is program for UNIX and GNU/Linux systems
which can post-process <ULINK
URL="http://www.ncbi.nlm.nih.gov/BLAST/">BLAST</ULINK> version 1 output into
@@ -165,7 +170,7 @@ cd ~/act
<PARA>
<COMMAND>
-java -Dartemis.environment=UNIX -classpath .:./lib/biojava.jar:./lib/jakarta-regexp-1.2.jar:./lib/jemAlign.jar -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ActMain
+ java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ActMain
</COMMAND>
</PARA>
</SECT1>
diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml
index 2cf4c84fd..2a51aba15 100644
--- a/docs/file_menu.sgml
+++ b/docs/file_menu.sgml
@@ -64,7 +64,7 @@ URL="http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/"><COMMAND>M
The output of <ULINK URL="http://www.ncbi.nlm.nih.gov/blast/">blastall version
2.2.2</ULINK> or better. <COMMAND>blastall</COMMAND> must be run with the
<COMMAND>-m 8</COMMAND> flag which generates one line of information per HSP.
-Note that currently &prog; displays each Blast HSP is a separate feature
+Note that currently &prog; displays each Blast HSP as a separate feature
rather than displaying each BLAST hit as a feature.
</PARA>
</LISTITEM>
diff --git a/docs/next_gen.sgml b/docs/next_gen.sgml
index a8d7bffbf..51a80c211 100644
--- a/docs/next_gen.sgml
+++ b/docs/next_gen.sgml
@@ -7,7 +7,7 @@ Java 1.6.
</PARA>
<PARA>
<ULINK URL="http://samtools.sourceforge.net/">BAM</ULINK> files need to be sorted and indexed using <ULINK
-URL="http://samtools.sourceforge.net/">samtools</ULINK>. The index file should be in
+URL="http://samtools.sourceforge.net/">SAMtools</ULINK>. The index file should be in
the same directory as the BAM file. This provides an integrated
<ULINK URL="http://bamview.sourceforge.net/">BamView</ULINK> panel in &prog;, displaying
sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded
--
GitLab