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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
author yhoogstrate
date Fri, 20 Nov 2015 11:04:43 -0500
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
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1 <?xml version="1.0"?>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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2 <tool_dependency>
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3 <package name="python" version="2.7">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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4 <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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5 </package>
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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7 <package name="htseq" version="0.6.1">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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8 <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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9 </package>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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11 <package name="fuma" version="2.11.0">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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12 <install version="1.0">
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13 <actions>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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14 <action type="download_by_url">https://github.com/yhoogstrate/fuma/archive/4b3432078949523f93e523c501f6ed813ee23d35.tar.gz</action>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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16 <action type="set_environment_for_install">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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17 <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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18 <package name="python" version="2.7" />
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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19 </repository>
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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21 <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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22 <package name="htseq" version="0.6.1" />
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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23 </repository>
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24 </action>
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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27 <action type="make_directory">$INSTALL_DIR/lib64/python</action>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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29 <action type="shell_command">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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31 python setup.py build &amp;&amp;
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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32 python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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33
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34 ## Tests fails because the import of unittest goes wrong:
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35 ## http://stackoverflow.com/questions/26893504/attributeerror-module-object-has-no-attribute-testcase
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36 ## python setup.py test
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37 </action>
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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39 <action type="set_environment">
f922f018f507 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
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40 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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42 </action>
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43 </actions>
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44 </install>
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45 <readme>
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46 Downloads and installs FuMa.
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47
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48 Prerequisites:
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49 - git
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50 </readme>
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51 </package>
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52 </tool_dependency>