Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_10
changeset 12:41de4f005517 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_10 commit 543b8d28d5f84f5b8ac31b3aa05f68a7b4094d66
| author | iuc |
|---|---|
| date | Mon, 25 May 2015 05:15:27 -0400 |
| parents | 9cf7e341af5d |
| children | 3b6bb451665c |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 89 insertions(+), 2 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon May 25 05:11:27 2015 -0400 +++ b/tool_dependencies.xml Mon May 25 05:15:27 2015 -0400 @@ -1,6 +1,93 @@ <?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="1.9"> + <repository changeset_revision="e5dd107dace7" 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="635f2c96e6e6" 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="5e063e84dfc5" 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="b1cd8e8b8346" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="bx-python" version="0.7.2"> + <repository changeset_revision="d5ca75285c8e" name="package_python_2_7_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> + <package name="python" version="2.7"> + <repository changeset_revision="00d2c3e43807" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="deepTools" version="1.5.10"> - <repository changeset_revision="a1ce63f65a5c" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> + <install version="1.0"> + <actions> + <action type="setup_python_environment"> + <repository changeset_revision="00d2c3e43807" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="python" version="2.7" /> + </repository> + <repository changeset_revision="b1cd8e8b8346" 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="d5ca75285c8e" 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="e5dd107dace7" 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="635f2c96e6e6" 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="5e063e84dfc5" 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"> + <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> + <package>https://github.com/fidelram/deepTools/archive/1.5.10.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</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</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">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable> + <!-- include scipy --> + <environment_variable action="prepend_to" name="PYTHONPATH">$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[PYTHONPATH_BX_PYTHON]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BX_PYTHON]</environment_variable> + <!-- include pysam --> + <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable> + <!-- include ucsc tools --> + <environment_variable action="prepend_to" name="PATH">$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>