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

@@ -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>

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>

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>

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