Mercurial > repos > yhoogstrate > package_pysam_0_8_2

annotate tool_dependencies.xml @ 0:b8d22acd3017 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
author yhoogstrate
date Thu, 21 May 2015 07:22:19 -0400
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children f8fecf1f6eba
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b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="ez_setup" version="0.9">
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4 <!--
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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5 If cross-toolshed depenencies become allowed use the following:
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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6 <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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7 -->
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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8 <repository changeset_revision="10fd2e2a9f2f" name="package_ez_setup_0_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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9 </package>
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10
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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11 <package name="pysam" version="0.8.2.1">
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12 <install version="1.0">
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13 <actions>
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14 <action md5sum="daf63c1665fa601fc942f050f334a627" type="download_by_url">https://pypi.python.org/packages/source/p/pysam/pysam-0.8.2.1.tar.gz</action>
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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15 <action type="set_environment_for_install">
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16 <!--
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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17 If cross-toolshed depenencies become allowed use the following:
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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18 <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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19 -->
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20 <repository changeset_revision="10fd2e2a9f2f" name="package_ez_setup_0_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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21 <package name="ez_setup" version="0.9" />
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22 </repository>
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23 </action>
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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24 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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25 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
b8d22acd3017 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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26 <action type="set_environment">
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27 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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29 <environment_variable action="set_to" name="PYSAM_PATH">$INSTALL_DIR</environment_variable>
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30 <environment_variable action="set_to" name="PYSAM_ROOT_PATH">$INSTALL_DIR</environment_variable>
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31 </action>
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32 </actions>
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33 </install>
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34 <readme>
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35 Installation of pysam, pyrex and python are required. The installation can be accessed via PYSAM_PATH.
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36 The PYSAM_PATH has to be within the PYTHONPATH to let python automatically load this library.
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37 </readme>
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38 </package>
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39 </tool_dependency>