Mercurial > repos > jjohnson > package_cistrome_2014_09_29

annotate tool_dependencies.xml @ 0:b9b48eb563d1 draft default tip

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Imported from capsule None
author jjohnson
date Tue, 14 Oct 2014 10:06:50 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="numpy" version="1.7.1">
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4 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="cython" version="0.20.1">
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7 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="cistrome" version="2014-09-29">
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10 <install version="1.0">
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11 <actions>
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12 <action type="shell_command">hg clone https://bitbucket.org/jjohnson/cistrome-applications-harvard cistrome</action>
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13 <action type="shell_command">hg update -d 2014-09-29</action>
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14 <action type="shell_command">cd cistrome-extra-apps &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
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15 <action type="shell_command">cd published-packages/CEAS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
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16 <action type="shell_command">cd published-packages/MA2C &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
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17 <!-- needs numpy -->
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18 <action type="set_environment_for_install">
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19 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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20 <package name="numpy" version="1.7.1" />
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21 </repository>
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22 </action>
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23 <action type="shell_command">cd published-packages/MACS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
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24 <action type="shell_command">cd published-packages/MAT &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
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25 <action type="shell_command">cd published-packages/NPS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
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26 <!-- needs numpy Cython -->
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27 <action type="set_environment_for_install">
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28 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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29 <package name="cython" version="0.20.1" />
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30 </repository>
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31 </action>
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32 <action type="shell_command">
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33 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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34 cd mdseqpos &amp;&amp;
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35 sed "s#/data/static_libraries/assembly/#$INSTALL_DIR/assembly/#" lib/settings.py.example &gt; lib/settings.py &amp;&amp;
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36 sed -i".tmp" "s#NUMPY_PATH = numpy#global NUMPY_PATH; NUMPY_PATH = numpy#" setup.py &amp;&amp;
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37 python setup.py install --home=$INSTALL_DIR
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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41 </action>
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42 <!-- this includes CistromeAP -->
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43 <action type="set_environment">
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44 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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45 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib64/python</environment_variable>
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46 </action>
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47 </actions>
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48 </install>
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49 <readme>
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50 Installs the cistrome applications code from https://bitbucket.org/cistrome/cistrome-applications-harvard
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51 ( branch for genome_dir option to override settings.py https://bitbucket.org/jjohnson/cistrome-applications-harvard )
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52 Runtime dependencies: bx-python, biopython, PIL, jinja2, MySQLdb
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53 </readme>
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54 </package>
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55 </tool_dependency>