changeset 10:2720b1e27a9c draft

Added dependency for infernal
author lionelguy
date Fri, 06 Sep 2013 05:38:49 -0400 (2013-09-06)
parents 37e2aeda27f4
children f2cc11ac2006
files prokka.xml readme.rst tool_dependencies.xml
diffstat 3 files changed, 4 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/prokka.xml	Fri Sep 06 02:50:44 2013 -0400
+++ b/prokka.xml	Fri Sep 06 05:38:49 2013 -0400
@@ -6,7 +6,7 @@
     <requirement type="package" version="2.60">prodigal</requirement>
     <requirement type="package" version="0.1">package_barrnap_0_1</requirement>
     <!-- <requirement type="package" version="4.1">signalp</requirement> -->
-    <!-- <requirement type="package" version="3.0">infernal</requirement> -->
+    <requirement type="package" version="1.1rc4">infernal</requirement>
     <requirement type="package" version="3.1b1">hmmer</requirement>
     <requirement type="package" version="2.2.26+">blast+</requirement>
     <requirement type="package">tbl2asn</requirement>
--- a/readme.rst	Fri Sep 06 02:50:44 2013 -0400
+++ b/readme.rst	Fri Sep 06 05:38:49 2013 -0400
@@ -9,7 +9,6 @@
 Note
 ----
 
-- **infernal** >= 1.1rc4 is an optional dependency to find non-coding RNAs. An executable is shipped with prokka.
 - **SignalP** >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, no automatic dependency is managed.
 - **tbl2asn** >= 21.0 is required. This dependency is not managed here. The reason is that versions are increasing very rapidly. The software can be downloaded from the NCBI ftp site ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/.
 - **BioPerl** >= 1.6 is required, but the dependency is not managed here, although it might in future. 
--- a/tool_dependencies.xml	Fri Sep 06 02:50:44 2013 -0400
+++ b/tool_dependencies.xml	Fri Sep 06 05:38:49 2013 -0400
@@ -15,9 +15,9 @@
   <package name="package_barrnap_0_1" version="0.1">
     <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
-  <!--<package name="infernal" version="1.1rc4">
-    <repository name="package_infernal_1_1rc4" owner="iuc" />
-  </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> --&gt;
     <package name="prokka" version="1.7">
       <install version="1.0">
 	<actions>