Mercurial > repos > devteam > package_freebayes_0_9_6_9608597d

diff tool_dependencies.xml @ 0:7615ee9e216d draft default tip

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Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
author devteam
date Mon, 16 Dec 2013 16:30:37 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Dec 16 16:30:37 2013 -0500
@@ -0,0 +1,47 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="i386" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>       
+                </actions>                
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/freebayes/freebayes-0.9.6_9608597d-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>       
+                </actions>                
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/freebayes/freebayes-0.9.6_9608597d-Darwin-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>       
+                </actions>         
+                <actions>
+                    <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
+                    <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
+                    <action type="shell_command">git submodule update --recursive</action>
+                    <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
+                    <action type="move_directory_files">
+                        <source_directory>bin</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+FreeBayes requires g++ and the standard C and C++ development libraries.
+Additionally, cmake is required for building the BamTools API.
+        </readme>
+    </package>
+</tool_dependency>
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