diff tool_dependencies.xml @ 4:5c0030f52b83 draft

Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation.

--- 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>