Mercurial > repos > bgruening > deeptools
diff tool_dependencies.xml @ 65:9bee2c86eeb1 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
| author | iuc |
|---|---|
| date | Mon, 25 May 2015 05:16:10 -0400 |
| parents | 627004611e98 |
| children | 1dbd76a58d8b |
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--- a/tool_dependencies.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/tool_dependencies.xml Mon May 25 05:16:10 2015 -0400 @@ -1,93 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="matplotlib" version="1.2.1"> - <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="scipy" version="0.12.0"> - <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pysam" version="0.7.7"> - <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="bx-python" version="0.7.1"> - <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="ucsc_tools" version="0.1"> - <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="deepTools" version="1.5.10"> + <repository changeset_revision="41de4f005517" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="deepTools" version="1.5.9"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pysam" version="0.7.7" /> - </repository> - <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="bx-python" version="0.7.1" /> - </repository> - <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="matplotlib" version="1.2.1" /> - </repository> - <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="scipy" version="0.12.0" /> - </repository> - <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="samtools" version="0.1.19" /> - </repository> - <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="ucsc_tools" version="0.1" /> - </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 $INSTALL_DIR/bin - </action> - - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> - <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable> - <!-- include samtools into PATH --> - <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable> - <!-- include numpy --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> - <!-- include matplotlib --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[MATPLOTLIB_LIB_PATH]</environment_variable> - <!-- include scipy --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable> - <!-- include bx-python --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable> - <!-- include pysam --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable> - <!-- include ucsc tools --> - <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable> - - <!-- disable the config file of deepTools --> - <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> - </action> - </actions> - </install> - <readme> - Installation of deepTools from Fidel Ramirez. - https://github.com/fidelram/deepTools - </readme> - </package> </tool_dependency>