# HG changeset patch
# User crs4
# Date 1389173377 18000
# Node ID 5c0030f52b83d83c5bf1c6b46cf17e5edbc201a3
# Parent  fffa1ae330aed2e5536ac502d044731b7f987465
Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation.

diff -r fffa1ae330ae -r 5c0030f52b83 prokka.xml
--- a/prokka.xml	Mon Dec 09 04:58:14 2013 -0500
+++ b/prokka.xml	Wed Jan 08 04:29:37 2014 -0500
@@ -1,15 +1,16 @@
-<tool id="prokka" name="Prokka" version="1.2.0">
+<tool id="prokka" name="Prokka" version="1.3.0">
   <description>prokaryotic genome annotation</description>
   <requirements>
     <requirement type="package" version="2.2.28">blast+</requirement>
     <requirement type="package" version="3.1b1">hmmer</requirement>
     <requirement type="package" version="1.2.36">aragorn</requirement>
     <requirement type="package" version="2.60">prodigal</requirement>
-    <requirement type="binary">tbl2asn</requirement>
+    <requirement type="package" version="22.4">tbl2asn</requirement>
     <requirement type="package" version="20131122">gnu_parallel</requirement>
     <requirement type="package" version="0.3">barrnap</requirement>
     <requirement type="package" version="1.1">infernal</requirement>
-    <requirement type="package" version="1.7">prokka</requirement>
+    <requirement type="package" version="0.1.4">minced</requirement>
+    <requirement type="package" version="1.8">prokka</requirement>
   </requirements>
   <version_command>prokka --version</version_command>
   <command>
@@ -193,7 +194,7 @@
 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
 .. _Cuccuru2013: http://orione.crs4.it/
 
-This tool uses `Prokka`_, which is licensed separately. Please cite Seemann T. Prokka: Prokaryotic Genome Annotation System (in preparation).
+This tool uses `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted*
 
 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
   </help>
diff -r fffa1ae330ae -r 5c0030f52b83 readme.rst
--- a/readme.rst	Mon Dec 09 04:58:14 2013 -0500
+++ b/readme.rst	Wed Jan 08 04:29:37 2014 -0500
@@ -11,30 +11,31 @@
 
 - Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
 - Perl modules: Bio::SeqIO from BioPerl_ >= 1.6.900, `XML::Simple`_;
-- tbl2asn_ >= 21.0 is required. This dependency is not managed here since versions are increasing very rapidly;
 - SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper.
 
 .. _BioPerl: http://search.cpan.org/dist/BioPerl/
 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
-.. _tbl2asn: http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
 
 Configuration
 -------------
 
-If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of threads allocated by the job runner according to the configuration of the job destination selected for this tool (see http://wiki.galaxyproject.org/Admin/Config/Jobs ).
+prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
 
-If instead you are using an older Galaxy release, you should add a line
+If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
+
+If instead you are using an older Galaxy release, you should also add a line
 
   GALAXY_SLOTS=N; export GALAXY_SLOTS
 
-(where N is the number of threads allocated by the job runner) to the file
+(where N is the number of CPU cores allocated by the job runner for this tool) to the file
 
   <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh
 
 Version history
 ---------------
 
+- Release 4 (prokka 1.3.0): Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 (requires Galaxy release_2013.11.04 or later). Update citation.
 - Release 3 (prokka 1.2.0): 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).
 - Release 2 (prokka 1.1.0): Merge the wrappers by CRS4 and Lionel Guy. Directly call prokka, remove prokka.py . Add 'locustag', 'increment', 'gffver', 'compliant', 'addgenes', 'genus', 'species', 'strain', 'plasmid', 'gcode', 'usegenus', 'metagenome', 'fast', 'evalue', 'norrna', 'notrna' params. Upgrade BLAST+ dependency to v. 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
 - Release 1 (prokka 1.0.1): Add txt output file. Use a definition list instead of a block quote in <help>. Correct 2 dependency minimum versions.
diff -r fffa1ae330ae -r 5c0030f52b83 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 09 04:58:14 2013 -0500
+++ b/tool_dependencies.xml	Wed Jan 08 04:29:37 2014 -0500
@@ -12,6 +12,9 @@
   <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="tbl2asn" version="22.4">
+    <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
   <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>
@@ -21,10 +24,14 @@
   <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">
+  <package name="minced" version="0.1.4">
+    <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="prokka" version="1.8">
     <install version="1.0">
       <actions>
         <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
+        <action target_filename="prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
@@ -39,8 +46,7 @@
 
 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/ );
-- tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 .
+- 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/ ).
 
 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>