Mercurial > repos > pjbriggs > ceas
comparison tool_dependencies.xml @ 0:8b25779ee261 draft
Uploaded initial version to test toolshed.
| author | pjbriggs |
|---|---|
| date | Wed, 28 Jan 2015 04:50:01 -0500 |
| parents | |
| children | 695d61decd06 |
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| -1:000000000000 | 0:8b25779ee261 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="python_mysqldb" version="1.2.5"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action> | |
| 7 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
| 8 <action type="shell_command"> | |
| 9 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
| 10 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin | |
| 11 </action> | |
| 12 <action type="set_environment"> | |
| 13 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | |
| 14 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 15 </action> | |
| 16 </actions> | |
| 17 </install> | |
| 18 <readme>Installs Python module MySQLdb 1.2.5</readme> | |
| 19 </package> | |
| 20 <!-- bx_python | |
| 21 This is cribbed from devteam's 'package_bx_python_0_7' in the main | |
| 22 toolshed: | |
| 23 https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7 | |
| 24 --> | |
| 25 <package name="bx_python" version="0.7.1"> | |
| 26 <install version="1.0"> | |
| 27 <actions> | |
| 28 <action type="setup_virtualenv"> | |
| 29 numpy==1.7.1 | |
| 30 bx-python==0.7.1 | |
| 31 </action> | |
| 32 <action type="set_environment"> | |
| 33 <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable> | |
| 34 </action> | |
| 35 </actions> | |
| 36 </install> | |
| 37 <readme> | |
| 38 Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be | |
| 39 accessed via BX_PYTHON_PATH. | |
| 40 </readme> | |
| 41 </package> | |
| 42 <!-- cistrome_ceas | |
| 43 Installs the version of CEAS package found in the Cistrome | |
| 44 distribution: | |
| 45 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview | |
| 46 --> | |
| 47 <package name="cistrome_ceas" version="1.0.2.d8c0751"> | |
| 48 <install version="1.0"> | |
| 49 <actions> | |
| 50 <action type="shell_command"> | |
| 51 hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas | |
| 52 </action> | |
| 53 <action type="shell_command"> | |
| 54 hg update d8c0751 | |
| 55 </action> | |
| 56 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
| 57 <action type="shell_command"> | |
| 58 cd published-packages/CEAS/ | |
| 59 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
| 60 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin | |
| 61 </action> | |
| 62 <action type="set_environment"> | |
| 63 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | |
| 64 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 65 </action> | |
| 66 </actions> | |
| 67 </install> | |
| 68 <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751, | |
| 69 datestamp 20140929), which includes ceasBW (a version of ceas which can | |
| 70 handle bigWig file input from MACS2. | |
| 71 | |
| 72 Cistrome code is at | |
| 73 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview | |
| 74 | |
| 75 The CEAS code is under the published-packages/CEAS/ subdirectory | |
| 76 | |
| 77 Cistrome data files and documentation can be found at | |
| 78 http://liulab.dfci.harvard.edu/CEAS/index.html | |
| 79 </readme> | |
| 80 </package> | |
| 81 </tool_dependency> |