Mercurial > repos > antmarge > singlefitness

changeset 2:3b7c93cec1f8 draft

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Uploaded tool dependencies
author antmarge
date Sat, 18 Mar 2017 18:41:28 -0400
parents 5f2dfd76e755
children 4837b523cab1
files tool_dependencies.xml
diffstat 1 files changed, 43 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Mar 18 18:41:28 2017 -0400
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool_dependency>
+
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="LINKYX_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="samtools-fpic" version="0.1.19">
+        <repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="bioperl" version="1.6.922">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="samtools-fpic" version="0.1.19" />
+                    </repository>
+                    <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                </action>
+                <action type="setup_perl_environment">
+                    
+                    <!-- allow downloading and installing an Perl package from cpan.org-->
+                    <package>XML::Parser</package>
+                    <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
+                    <package>Bio::DB::Fasta</package>
+                    <package>File::Slurp</package>
+                    <package>Bio::DB::Sam</package>
+                    <package>PerlIO::gzip</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Bundle::BioPerl
+        </readme>
+    </package>
+</tool_dependency>