Mercurial > repos > iuc > package_gemini_0_9_1
changeset 3:610ebefc0db1 draft
Uploaded
| author | iuc |
|---|---|
| date | Sat, 16 Aug 2014 09:22:06 -0400 |
| parents | 8000d616c600 |
| children | a10ebb5a71bb |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 8 insertions(+), 57 deletions(-) [+] |
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--- a/tool_dependencies.xml Thu Aug 07 11:32:03 2014 -0400 +++ b/tool_dependencies.xml Sat Aug 16 09:22:06 2014 -0400 @@ -1,77 +1,28 @@ <?xml version="1.0"?> <tool_dependency> - <package name="grabix" version="0.1.3"> - <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="tabix" version="0.2.6"> - <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="bedtools" version="2.19.1"> - <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pybedtools" version="0.6.6"> - <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="bx-python" version="0.7.1"> - <repository changeset_revision="35e2457234ef" name="package_bx_python_0_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="scipy" version="0.12.0"> - <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pandas" version="0.14.1"> - <repository changeset_revision="21afd61aae1e" name="package_pandas_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="gemini" version="0.9.1"> <install version="1.0"> <actions> <!-- first action is always downloading --> - <action type="download_by_url">https://github.com/arq5x/gemini/archive/v0.9.1.tar.gz</action> + <action type="download_by_url">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action> <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="scipy" version="0.12.0" /> - </repository> - <repository changeset_revision="21afd61aae1e" name="package_pandas_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pandas" version="0.14.1" /> - </repository> - <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="tabix" version="0.2.6" /> - </repository> - <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="grabix" version="0.1.3" /> - </repository> - <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pybedtools" version="0.6.6" /> - </repository> - <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="bx-python" version="12-2013" /> - </repository> - <repository changeset_revision="35e2457234ef" name="package_bx_python_0_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="bx-python" version="0.7.1" /> + <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> </repository> </action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata </action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="PYTHONPATH_GEMINI">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="set_to" name="PATH_GEMINI">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable> <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable> </action> </actions>