Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 21:ff58cb74118d draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty
author yhoogstrate
date Fri, 28 Aug 2015 09:15:00 -0400
parents c0b7bf565723
children b38e4886f937
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20:c0b7bf565723 21:ff58cb74118d
38 <action type="shell_command"> 38 <action type="shell_command">
39 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ; 39 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
40 40
41 python setup.py install --root $INSTALL_DIR &amp;&amp; 41 python setup.py install --root $INSTALL_DIR &amp;&amp;
42 export SUB_DIR=$(dirname $(which python)) &amp;&amp; 42 export SUB_DIR=$(dirname $(which python)) &amp;&amp;
43 echo $SUB_DIR &amp;&amp; 43 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
44 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin &amp;&amp; 44 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin
45 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib
46 </action> 45 </action>
47 46
48 <action type="set_environment"> 47 <action type="set_environment">
49 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable> 48 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable>
50 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python"</environment_variable>
51 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
52 50
53 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable> 51 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
54 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> 52 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
55 </action> 53 </action>