Mercurial > repos > bgruening > bismark

changeset 2:82814a8a2395 draft

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added samtools 0.1.19 as dependency
author bgruening
date Wed, 21 Aug 2013 05:19:54 -0400
parents 9d02cd7883ad
children 91f07ff056ca
files bismark_bowtie2_wrapper.xml bismark_bowtie_wrapper.xml bismark_wrapper.py tool_dependencies.xml
diffstat 4 files changed, 6 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/bismark_bowtie2_wrapper.xml	Sat Jul 06 10:04:23 2013 -0400
+++ b/bismark_bowtie2_wrapper.xml	Wed Aug 21 05:19:54 2013 -0400
@@ -1,10 +1,10 @@
-<tool id="bismark_bowtie2" name="Bismark" version="0.7.12">
+<tool id="bismark_bowtie2" name="Bismark" version="0.7.12.1">
     <!-- Wrapper compatible with Bismark version 0.7.11 -->
     <description>bisulfite mapper (bowtie2)</description>
     <!--<version_command>bismark version</version_command>-->
     <requirements>
         <requirement type="set_environment">SCRIPT_PATH</requirement>
-        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="2.1.0">bowtie2</requirement>
     </requirements>
     <parallelism method="basic"></parallelism>
--- a/bismark_bowtie_wrapper.xml	Sat Jul 06 10:04:23 2013 -0400
+++ b/bismark_bowtie_wrapper.xml	Wed Aug 21 05:19:54 2013 -0400
@@ -1,10 +1,10 @@
-<tool id="bismark_bowtie" name="Bismark" version="0.7.12">
+<tool id="bismark_bowtie" name="Bismark" version="0.7.12.1">
     <!-- Wrapper compatible with Bismark version 0.7.11 -->
     <description>bisulfite mapper (bowtie)</description>
     <!--<version_command>bismark version</version_command>-->
     <requirements>
         <requirement type="set_environment">SCRIPT_PATH</requirement>
-        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="0.12.8">bowtie</requirement>
     </requirements>
     <parallelism method="basic"></parallelism>
--- a/bismark_wrapper.py	Sat Jul 06 10:04:23 2013 -0400
+++ b/bismark_wrapper.py	Wed Aug 21 05:19:54 2013 -0400
@@ -285,7 +285,6 @@
                 pass
 
             raise Exception, stderr
-
         tmp_stdout.close()
         tmp_stderr.close()
 
--- a/tool_dependencies.xml	Sat Jul 06 10:04:23 2013 -0400
+++ b/tool_dependencies.xml	Wed Aug 21 05:19:54 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="a7936f4ea405" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="cb87eae7fc3e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>