Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 17:823f0b1beccd 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 08:49:15 -0400
parents 0bd9a115e58a
children 40758e611549
comparison
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16:0bd9a115e58a 17:823f0b1beccd
34 34
35 Using - - root places the installation in: 35 Using - - root places the installation in:
36 $INSTALL_DIR / (python path dir) / 36 $INSTALL_DIR / (python path dir) /
37 --> 37 -->
38 <action type="shell_command"> 38 <action type="shell_command">
39 39 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
40 40
41 echo "a" ; 41 python setup.py install --root $INSTALL_DIR &amp;&amp;
42 echo "b" &amp;&amp; 42 mv $INSTALL_DIR$(which python)/bin $INSTALL_DIR/bin &amp;&amp;
43 echo "c" ; 43 mv $INSTALL_DIR$(which python)/lib $INSTALL_DIR/lib
44
45 <!--
46 comment
47 -->
48
49 echo "d" ;
50 echo "e" &amp;&amp;
51 echo "f"
52
53 </action> 44 </action>
54 45
55 <action type="set_environment"> 46 <action type="set_environment">
56 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable> 47 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
57 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python"</environment_variable> 48 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python"</environment_variable>
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable> 49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
59 50
60 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable> 51 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
61 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> 52 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
62 </action> 53 </action>
63 </actions> 54 </actions>