Mercurial > repos > bgruening > bismark

changeset 5:045c0592c180 draft

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Uploaded
author bgruening
date Sat, 13 Oct 2012 02:58:26 -0400
parents a4bd52c4ed46
children 1c97427d28a3
files bismark_wrapper/tool_dependencies.xml
diffstat 1 files changed, 1 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/bismark_wrapper/tool_dependencies.xml	Fri Oct 12 09:31:36 2012 -0400
+++ b/bismark_wrapper/tool_dependencies.xml	Sat Oct 13 02:58:26 2012 -0400
@@ -1,8 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!-- http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_v0.7.7.tar.gz -->
     <package name="bowtie2" version="2.0.0-beta7">
-        <install version="1.1">
+        <install version="1.0">
             <actions>
                 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
                 <action type="shell_command">make</action>
@@ -23,25 +22,4 @@
 Compiling bowtie2 requires zlib and libpthread to be present on your system.
         </readme>
     </package>
-    <!-- We ship bismark with that wrapper, so we only need to set the PATH variable -->
-    <package name="bismark">
-        <install version="1.1">
-                <action type="move_file">
-                    <source>bismark</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bismark_genome_preparation</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bismark_methylation_extractor</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">./</environment_variable>
-                </action>
-            </actions>
-        </install>
-    </package>
 </tool_dependency>