Mercurial > repos > bgruening > deeptools
comparison tool_dependencies.xml @ 30:2e5b92e7f3cb draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 28 Jan 2014 13:54:34 -0500 |
| parents | 60788be7b346 |
| children | 934b9fccabd4 |
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| 29:60788be7b346 | 30:2e5b92e7f3cb |
|---|---|
| 8 </package> | 8 </package> |
| 9 <package name="matplotlib" version="1.2.1"> | 9 <package name="matplotlib" version="1.2.1"> |
| 10 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 10 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> |
| 11 </package> | 11 </package> |
| 12 <package name="scipy" version="0.12.0"> | 12 <package name="scipy" version="0.12.0"> |
| 13 <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 13 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> |
| 14 </package> | 14 </package> |
| 15 <package name="pysam" version="0.7.7"> | 15 <package name="pysam" version="0.7.7"> |
| 16 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 16 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> |
| 17 </package> | 17 </package> |
| 18 <package name="bx-python" version="12-2013"> | 18 <package name="bx-python" version="12-2013"> |
| 55 </actions> | 55 </actions> |
| 56 </install> | 56 </install> |
| 57 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> | 57 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> |
| 58 </package> | 58 </package> |
| 59 | 59 |
| 60 <package name="deepTools" version="1.5.4_e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61"> | 60 <package name="deepTools" version="1.5.4_eabc1c3842f4b6367fb41904061a3b95c9a0ce0c"> |
| 61 <install version="1.0"> | 61 <install version="1.0"> |
| 62 <actions> | 62 <actions> |
| 63 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> | 63 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> |
| 64 <!-- populate the environment variables from the dependend repos --> | 64 <!-- populate the environment variables from the dependend repos --> |
| 65 <action type="set_environment_for_install"> | 65 <action type="set_environment_for_install"> |
| 73 <package name="numpy" version="1.7.1" /> | 73 <package name="numpy" version="1.7.1" /> |
| 74 </repository> | 74 </repository> |
| 75 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | 75 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> |
| 76 <package name="matplotlib" version="1.2.1" /> | 76 <package name="matplotlib" version="1.2.1" /> |
| 77 </repository> | 77 </repository> |
| 78 <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | 78 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> |
| 79 <package name="scipy" version="0.12.0" /> | 79 <package name="scipy" version="0.12.0" /> |
| 80 </repository> | 80 </repository> |
| 81 </action> | 81 </action> |
| 82 <action type="shell_command">git reset --hard e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61</action> | 82 <action type="shell_command">git reset --hard eabc1c3842f4b6367fb41904061a3b95c9a0ce0c</action> |
| 83 <action type="make_directory">$INSTALL_DIR/lib/python</action> | 83 <action type="make_directory">$INSTALL_DIR/lib/python</action> |
| 84 <action type="shell_command"> | 84 <action type="shell_command"> |
| 85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | 85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && |
| 86 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin | 86 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin |
| 87 </action> | 87 </action> |