Mercurial > repos > bgruening > deeptools
comparison tool_dependencies.xml @ 17:32bb3debd588 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 06 Dec 2013 11:28:08 -0500 |
| parents | 351cd1f8791b |
| children | 63eb0e2ea7de |
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| 16:d0667be9cb0c | 17:32bb3debd588 |
|---|---|
| 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" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 13 <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" 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" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 16 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> |
| 17 </package> | |
| 18 <package name="bx-python" version="12_2013"> | |
| 19 <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | |
| 17 </package> | 20 </package> |
| 18 | 21 |
| 19 <package name="ucsc_tools" version="0.1"> | 22 <package name="ucsc_tools" version="0.1"> |
| 20 <install version="1.0"> | 23 <install version="1.0"> |
| 21 <actions> | 24 <actions> |
| 52 </actions> | 55 </actions> |
| 53 </install> | 56 </install> |
| 54 <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> |
| 55 </package> | 58 </package> |
| 56 | 59 |
| 57 <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a"> | 60 <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e"> |
| 58 <install version="1.0"> | 61 <install version="1.0"> |
| 59 <actions> | 62 <actions> |
| 63 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> | |
| 60 <!-- populate the environment variables from the dependend repos --> | 64 <!-- populate the environment variables from the dependend repos --> |
| 61 <action type="set_environment_for_install"> | 65 <action type="set_environment_for_install"> |
| 62 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | 66 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> |
| 63 <package name="pysam" version="0.7.7" /> | 67 <package name="pysam" version="0.7.7" /> |
| 64 </repository> | 68 </repository> |
| 69 <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | |
| 70 <package name="bx-python" version="12-2013" /> | |
| 71 </repository> | |
| 65 </action> | 72 </action> |
| 66 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> | 73 <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action> |
| 67 <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action> | |
| 68 <action type="make_directory">$INSTALL_DIR/lib/python</action> | 74 <action type="make_directory">$INSTALL_DIR/lib/python</action> |
| 69 <action type="shell_command"> | 75 <action type="shell_command"> |
| 70 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | 76 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && |
| 71 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin | 77 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin |
| 72 </action> | 78 </action> |
| 73 | |
| 74 <action type="set_environment"> | 79 <action type="set_environment"> |
| 75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | 80 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
| 76 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | 81 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> |
| 77 <!-- disable the config file of deepTools --> | 82 <!-- disable the config file of deepTools --> |
| 78 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> | 83 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> |
| 79 </action> | 84 </action> |
| 80 </actions> | 85 </actions> |
| 81 </install> | 86 </install> |
| 82 <readme>Installation of deepTools from Fidel Ramirez.</readme> | 87 <readme> |
| 88 Installation of deepTools from Fidel Ramirez. | |
| 89 https://github.com/fidelram/deepTools | |
| 90 </readme> | |
| 83 </package> | 91 </package> |
| 84 </tool_dependency> | 92 </tool_dependency> |