Mercurial > repos > yhoogstrate > package_fuma_2_10_1

changeset 0:bd66bc0860db draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
author yhoogstrate
date Tue, 20 Oct 2015 10:11:38 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 55 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 10:11:38 2015 -0400
@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="2.7">
+        <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="htseq" version="0.6.1">
+        <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="fuma" version="2.10.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://github.com/yhoogstrate/fuma/archive/6b79b9a958212b900dedda0247f84f696f81ec89.tar.gz</action>
+                
+                <action type="set_environment_for_install">
+                     <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="python" version="2.7" />
+                    </repository>
+                    
+                   <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="htseq" version="0.6.1" />
+                    </repository>
+                </action>
+                
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
+                
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
+                    python setup.py build                                                           &amp;&amp;
+                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
+                    
+                    ## Tests fails because the import of unittest goes wrong:
+                    ## http://stackoverflow.com/questions/26893504/attributeerror-module-object-has-no-attribute-testcase
+                    ## python setup.py test
+                </action>
+                
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    
+                    <environment_variable action="set_to" name="FUMA_PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="FUMA_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Downloads and installs FuMa.
+            
+            Prerequisites:
+                - git
+        </readme>
+    </package>
+</tool_dependency>