Mercurial > repos > yhoogstrate > package_fuma_2_12_3

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
author yhoogstrate
date Wed, 16 Mar 2016 08:04:29 -0400
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b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
yhoogstrate
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1 <?xml version="1.0"?>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
yhoogstrate
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2 <tool_dependency>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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3 <package name="python" version="2.7">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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4 <repository changeset_revision="409e51c1c555" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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5 </package>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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7 <package name="htseq" version="0.6.1">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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8 <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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9 </package>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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10
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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11 <package name="fuma" version="2.12.3">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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12 <install version="1.0">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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13 <actions>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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14 <action sha256sum="8a7bbddfee926170de3766f6991ef92e5e2ce5f5cf4a42784cb54875d2d8b978" type="download_by_url">https://github.com/yhoogstrate/fuma/archive/v2.12.3.tar.gz</action>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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16 <action type="set_environment_for_install">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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17 <repository changeset_revision="409e51c1c555" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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18 <package name="python" version="2.7" />
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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19 </repository>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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21 <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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22 <package name="htseq" version="0.6.1" />
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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23 </repository>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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24 </action>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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27 <action type="make_directory">$INSTALL_DIR/lib64/python</action>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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28
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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29 <action type="shell_command">
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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31 python setup.py build &amp;&amp;
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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32 python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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33
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34 ## Tests fails because the import of unittest goes wrong:
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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35 ## http://stackoverflow.com/questions/26893504/attributeerror-module-object-has-no-attribute-testcase
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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36 ## python setup.py test
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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37 </action>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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39 <action type="set_environment">
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40 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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42 </action>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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43 </actions>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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44 </install>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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45 <readme>
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46 Downloads and installs FuMa (FusionMatcher).
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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47 </readme>
b17419f5c8c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 071a56796af75a1ae3ddc9bced9b345039d0ef94
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48 </package>
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49 </tool_dependency>