# HG changeset patch
# User crs4
# Date 1443723246 14400
# Node ID f5e44aad649808332473035a8253afaa7b0a830d
# Parent  3ad7ef0ba385b9a764cb677493b19f012b268225
Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.

diff -r 3ad7ef0ba385 -r f5e44aad6498 COPYING
--- a/COPYING	Mon Oct 27 06:45:52 2014 -0400
+++ b/COPYING	Thu Oct 01 14:14:06 2015 -0400
@@ -1,8 +1,9 @@
+Copyright © 2015 The Genome Analysis Centre http://www.tgac.ac.uk/
 Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
 Copyright © 2013 Lionel Guy
 Created by:
 Paolo Uva <paolo.uva@crs4.it>
-Nicola Soranzo <nicola.soranzo@crs4.it>
+Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
 Lionel Guy <lionel.guy@icm.uu.se>
 Philip Mabon <philipmabon@gmail.com>
 
diff -r 3ad7ef0ba385 -r f5e44aad6498 prokka.xml
--- a/prokka.xml	Mon Oct 27 06:45:52 2014 -0400
+++ b/prokka.xml	Thu Oct 01 14:14:06 2015 -0400
@@ -1,16 +1,16 @@
-<tool id="prokka" name="Prokka" version="1.4.0">
+<tool id="prokka" name="Prokka" version="1.11.0">
   <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="2.2.31">blast+</requirement>
+    <requirement type="package" version="3.1b2">hmmer</requirement>
     <requirement type="package" version="1.2.36">aragorn</requirement>
     <requirement type="package" version="2.60">prodigal</requirement>
-    <requirement type="package" version="23.7">tbl2asn</requirement>
+    <requirement type="package" version="24.3">tbl2asn</requirement>
     <requirement type="package" version="20131122">gnu_parallel</requirement>
-    <requirement type="package" version="0.5">barrnap</requirement>
+    <requirement type="package" version="0.7">barrnap</requirement>
     <requirement type="package" version="1.1">infernal</requirement>
     <requirement type="package" version="0.1.6">minced</requirement>
-    <requirement type="package" version="1.10">prokka</requirement>
+    <requirement type="package" version="1.11">prokka</requirement>
   </requirements>
   <version_command>prokka --version</version_command>
   <command>
@@ -200,16 +200,6 @@
 You can use this tool only if you agree to the license terms of: `Prokka`_.
 
 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
-
-If you use this tool, please cite:
-
-- |Cuccuru2014|_
-- |Seemann2014|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
-.. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069
-.. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068
   </help>
   <citations>
     <citation type="doi">10.1093/bioinformatics/btu135</citation>
diff -r 3ad7ef0ba385 -r f5e44aad6498 readme.rst
--- a/readme.rst	Mon Oct 27 06:45:52 2014 -0400
+++ b/readme.rst	Thu Oct 01 14:14:06 2015 -0400
@@ -24,17 +24,10 @@
 
 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 CPU cores allocated by the job runner for this tool) to the file
-
-  <tool_dependencies_dir>/prokka/1.10/crs4/prokka/<hash_string>/env.sh
-
 Version history
 ---------------
 
+- Release 7 (prokka 1.11.0): Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.
 - Release 6 (prokka 1.4.0): Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation.
 - 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.
diff -r 3ad7ef0ba385 -r f5e44aad6498 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 27 06:45:52 2014 -0400
+++ b/tool_dependencies.xml	Thu Oct 01 14:14:06 2015 -0400
@@ -1,25 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="blast+" version="2.2.28">
-    <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="blast+" version="2.2.31">
+    <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="hmmer" version="3.1b1">
-    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="hmmer" version="3.1b2">
+    <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="aragorn" version="1.2.36">
     <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="prodigal" version="2.60">
-    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="9ec3f1e9198e" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="tbl2asn" version="23.7">
-    <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="tbl2asn" version="24.3">
+    <repository changeset_revision="41764d6a6a3c" name="package_tbl2asn_24_3" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="gnu_parallel" version="20131122">
     <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="barrnap" version="0.5">
-    <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="barrnap" version="0.7">
+    <repository changeset_revision="c46ab932a19b" name="package_barrnap_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="infernal" version="1.1">
     <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -27,10 +27,10 @@
   <package name="minced" version="0.1.6">
     <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="prokka" version="1.10">
+  <package name="prokka" version="1.11">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
+        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.11.tar.gz</action>
         <action type="shell_command">bin/prokka --setupdb</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
@@ -42,13 +42,11 @@
       </actions>
     </install>
     <readme>
-Warning: Prokka includes custom databases and is thus about a 340 MB download!
+Warning: Prokka includes custom databases and is thus about a 360 MB 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/ ).
-
-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>