Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_10
diff tool_dependencies.xml @ 1:fde32464913e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_10 commit 5a986267144da2093f820e1833325fd3d5902c7d-dirty
| author | iuc |
|---|---|
| date | Sun, 17 May 2015 16:35:04 -0400 |
| parents | 6a8a27d4992b |
| children | f5929e04efc6 |
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--- a/tool_dependencies.xml Sun May 17 15:01:25 2015 -0400 +++ b/tool_dependencies.xml Sun May 17 16:35:04 2015 -0400 @@ -4,13 +4,13 @@ <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="1.9"> - <repository changeset_revision="a095a5975d3a" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1b7d6172a358" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="matplotlib" version="1.4"> <repository changeset_revision="652ee3afbd12" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="scipy" version="0.14"> - <repository changeset_revision="8d22fd5a704c" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b24af010d80a" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="pysam" version="0.8.3"> <repository changeset_revision="d2acc22011f9" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> @@ -21,24 +21,29 @@ <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> + <package name="python" version="2.7"> + <repository changeset_revision="55bebb0e06ec" name="package_python_2_7" owner="iuc" prior_installation_required="True" 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"> + <action type="setup_python_environment"> + <repository changeset_revision="55bebb0e06ec" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="python" version="2.7" /> + </repository> <repository changeset_revision="d2acc22011f9" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="pysam" version="0.8.3" /> </repository> <repository changeset_revision="2ded28a666c7" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="bx-python" version="0.7.2" /> </repository> - <repository changeset_revision="a095a5975d3a" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="1b7d6172a358" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="numpy" version="1.9" /> </repository> <repository changeset_revision="652ee3afbd12" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="matplotlib" version="1.4" /> </repository> - <repository changeset_revision="8d22fd5a704c" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="b24af010d80a" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="scipy" version="0.14" /> </repository> <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> @@ -47,16 +52,12 @@ <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 $INSTALL_DIR/bin + <package>https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</package> </action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</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>