diff tool_dependencies.xml @ 3:fffa1ae330ae draft

Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later).

--- a/tool_dependencies.xml	Fri Oct 25 08:59:51 2013 -0400
+++ b/tool_dependencies.xml	Mon Dec 09 04:58:14 2013 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <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" />
+    <repository changeset_revision="23b9ba41ad00" 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" />
@@ -12,11 +12,14 @@
   <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 name="gnu_parallel" version="20131122">
+    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" 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 name="barrnap" version="0.3">
+    <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="infernal" version="1.1">
+    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="prokka" version="1.7">
     <install version="1.0">
@@ -29,9 +32,6 @@
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
         </action>
-        <action type="set_environment">
-          <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable>
-        </action>
       </actions>
     </install>
     <readme>
@@ -40,12 +40,9 @@
 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/ );
-- Prodigal ( http://prodigal.ornl.gov/ ) &gt;= 2.60 ;
-- tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ;
-- GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ;
-- Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 .
+- tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 .
 
-Configuration: Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).
+Configuration: Previously (until Release 2), the PROKKA_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of CPUs to use (--cpus). This is not used anymore and may be removed.
     </readme>
   </package>
 </tool_dependency>