Mercurial > repos > yhoogstrate > package_crossmap_0_2

diff tool_dependencies.xml @ 1:803db5577b07 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
author yhoogstrate
date Fri, 28 Aug 2015 03:43:49 -0400
parents 805c8fbd3b4e
children e4de7f1284ce
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--- a/tool_dependencies.xml	Wed Aug 26 11:03:59 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 28 03:43:49 2015 -0400
@@ -1,11 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="nose" version="1.3.7">
+        <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
     <package name="numpy" version="1.9">
         <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     
-    <package name="cython" version="0.20.1">
-        <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="cython" version="0.23.1">
+        <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="crossmap" version="0.2">
@@ -14,8 +18,11 @@
                 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
                 
                 <action type="setup_python_environment">
-                    <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="cython" version="0.20.1" />
+                    <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="nose" version="1.3.7" />
+                    </repository>
+                    <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="cython" version="0.23.1" />
                     </repository>
                     <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.9" />
@@ -28,6 +35,8 @@
                 <action type="shell_command">
                     sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
                     
+                    export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp;
+                    export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp;
                     export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
                     
                     python setup.py install --root $INSTALL_DIR