Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 4:dbe83f5bef40 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
author yhoogstrate
date Thu, 12 Nov 2015 16:07:42 -0500
parents bbc4d67d6a37
children
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3:bbc4d67d6a37 4:dbe83f5bef40
36 <!-- If CrossMap is installed with - - home or - - prefix 36 <!-- If CrossMap is installed with - - home or - - prefix
37 it often crashes with a 'write-test' error 37 it often crashes with a 'write-test' error
38 38
39 Using - - root places the installation in: 39 Using - - root places the installation in:
40 $INSTALL_DIR / (python path dir) / 40 $INSTALL_DIR / (python path dir) /
41
42
43 The setuptools shipped with galaxy's python version crashes if
44 a setuptools installation contains a setup_requires tag
41 --> 45 -->
42 <action type="shell_command"> 46 <action type="shell_command">
43 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ; 47 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
48 sed -i.bak -r "s/setup_requires/#setup_requires/" "setup.py" ;
44 49
45 python setup.py install --root $INSTALL_DIR &amp;&amp; 50 python setup.py install --root $INSTALL_DIR &amp;&amp;
46 export SUB_DIR=$(dirname $(which python)) &amp;&amp; 51 export SUB_DIR=$(dirname $(which python)) &amp;&amp;
47 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp; 52 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
48 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin 53 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin