diff tool_dependencies.xml @ 2:4bafaa074484 draft

Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .

--- a/tool_dependencies.xml	Thu Sep 26 12:39:52 2013 -0400
+++ b/tool_dependencies.xml	Fri Oct 25 08:59:51 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="blast+" version="2.2.26+">
-    <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <package name="blast+" version="2.2.28">
+    <repository changeset_revision="ed85ca8e4295" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="hmmer" version="3.1b1">
     <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
@@ -9,13 +9,19 @@
   <package name="aragorn" version="1.2.36">
     <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
+  <package name="prodigal" version="2.60">
+    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="barrnap" version="0.2">
+    <repository changeset_revision="8ab7a17861ea" name="package_barrnap_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
   <package name="infernal" version="1.1rc4">
     <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="prokka" version="1.7">
     <install version="1.0">
       <actions>
-        <action target_filename="" type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
+        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
@@ -29,6 +35,8 @@
       </actions>
     </install>
     <readme>
+Warning: Prokka includes custom databases and is thus about a 2.0 GB download!
+
 Dependencies of Prokka which needs to be installed separately:
 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
 - Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) &gt;= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ );
@@ -37,9 +45,7 @@
 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ;
 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 .
 
-Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).
-
-Note: Prokka is about a 2.0 GB download due to included custom databases.
+Configuration: Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).
     </readme>
   </package>
 </tool_dependency>