diff tool_dependencies.xml @ 0:95505a9fa26f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 10 13:11:26 2013 -0400
@@ -0,0 +1,45 @@
+<?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>
+  <package name="hmmer" version="3.1b1">
+    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://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="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="move_directory_files">
+          <source_directory>.</source_directory>
+          <destination_directory>$INSTALL_DIR</destination_directory>
+        </action>
+        <action type="set_environment">
+          <environment_variable action="prepend_to" name="PATH">$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>
+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;= 1.6.1, 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;= 20120322 ;
+- 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.
+    </readme>
+  </package>
+</tool_dependency>