Mercurial > repos > biomonika > linkyx

changeset 31:03782fcd1552

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
rename samtools dependency to samtools--fpic
author biomonika
date Tue, 10 Feb 2015 11:46:12 -0500
parents 57b2221536fc
children cf7cd22fc5d3
files LINKYX_identify_X_linked_SNPs.xml LINKYX_identify_Y_linked_SNPs.xml LINKYX_mpileup_wrapper.xml LINKYX_reformat_trinity_header.xml sort_bam.xml tool_dependencies.xml
diffstat 6 files changed, 29 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/LINKYX_identify_X_linked_SNPs.xml	Tue Feb 10 11:33:33 2015 -0500
+++ b/LINKYX_identify_X_linked_SNPs.xml	Tue Feb 10 11:46:12 2015 -0500
@@ -3,7 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools-fpic</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $output1 $output2 $output3 $output4 $output5</command>
--- a/LINKYX_identify_Y_linked_SNPs.xml	Tue Feb 10 11:33:33 2015 -0500
+++ b/LINKYX_identify_Y_linked_SNPs.xml	Tue Feb 10 11:46:12 2015 -0500
@@ -3,7 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools-fpic</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command>
--- a/LINKYX_mpileup_wrapper.xml	Tue Feb 10 11:33:33 2015 -0500
+++ b/LINKYX_mpileup_wrapper.xml	Tue Feb 10 11:46:12 2015 -0500
@@ -3,7 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools-fpic</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_mpileup_wrapper.sh $output $input1 $input2</command>
--- a/LINKYX_reformat_trinity_header.xml	Tue Feb 10 11:33:33 2015 -0500
+++ b/LINKYX_reformat_trinity_header.xml	Tue Feb 10 11:46:12 2015 -0500
@@ -3,7 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools-fpic</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_reformat_trinity_header.sh $output $input1</command>
--- a/sort_bam.xml	Tue Feb 10 11:33:33 2015 -0500
+++ b/sort_bam.xml	Tue Feb 10 11:46:12 2015 -0500
@@ -3,7 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools-fpic</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">sort_bam.sh $output $input1</command>
--- a/tool_dependencies.xml	Tue Feb 10 11:33:33 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 10 11:46:12 2015 -0500
@@ -1,36 +1,40 @@
 <?xml version="1.0"?>
 <tool_dependency>
+
     <set_environment version="1.0">
         <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
 
-  <package name="perl" version="5.18.1">
-      <repository changeset_revision="" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
+    <package name="perl" version="5.18.1">
+        <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-fpic" 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="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="" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                      <package name="perl" version="5.18.1" />
+    <package name="bioperl" version="1.6.922">
+        <install version="1.0">
+            <actions>
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="" name="package_samtools_0_1_19_custom" owner="biomonika" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="samtools-fpic" version="0.1.19" />
+                    </repository>
+                    <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-->
-                   <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>
+                    <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>
+    </package>
 </tool_dependency>