Mercurial > repos > biomonika > linkyx

changeset 30:57b2221536fc

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remove custom samtools package to its own package on TTS
author biomonika
date Tue, 10 Feb 2015 11:33:33 -0500
parents ba6849a9389e
children 03782fcd1552
files tool_dependencies.xml
diffstat 1 files changed, 10 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Feb 10 10:54:44 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 10 11:33:33 2015 -0500
@@ -5,13 +5,18 @@
     </set_environment>
 
   <package name="perl" version="5.18.1">
-      <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bioperl" version="1.6.922">
+      <repository changeset_revision="" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+
+  <package name="samtools" version="0.1.19">
+      <repository changeset_revision="" name="package_samtools_0_1_19_custom" owner="biomonika" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+
+  <package name="bioperl" version="1.6.922">
       <install version="1.0">
           <actions>
               <action type="setup_perl_environment">
-                  <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                  <repository changeset_revision="" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                       <package name="perl" version="5.18.1" />
                     </repository>
                     <!-- allow downloading and installing an Perl package from cpan.org-->
@@ -27,20 +32,5 @@
         <readme>
             Bundle::BioPerl
         </readme>
-    </package>
-
-    <package name="samtools" version="0.1.19">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
-                <action type="shell_command">sed -i 's/O2/O2 -fPIC/' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
-    </package>
+  </package>
 </tool_dependency>