# HG changeset patch # User bgruening # Date 1442603421 14400 # Node ID 6f4f0a2406f61946d5f59c2da031534264991fcf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_11 commit 999fd0b109aae24b72ce5791b7965941e9b2a19a-dirty diff -r 000000000000 -r 6f4f0a2406f6 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 18 15:10:21 2015 -0400 @@ -0,0 +1,92 @@ +<?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="8d42102c4e36" 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="345685d467fb" 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="7002d3382856" 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="dd8ace13f3aa" 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="ed5fdaba090a" 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="d31e73183b94" name="package_ucsc_tools_0_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="python" version="2.7.10"> + <repository changeset_revision="08162f8bc496" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="deepTools" version="1.5.11"> + <install version="1.0"> + <actions> + <action type="setup_python_environment"> + <repository changeset_revision="08162f8bc496" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="python" version="2.7.10" /> + </repository> + <repository changeset_revision="dd8ace13f3aa" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.8.3" /> + </repository> + <repository changeset_revision="ed5fdaba090a" name="package_python_2_7_bx_python_0_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="bx-python" version="0.7.2" /> + </repository> + <repository changeset_revision="8d42102c4e36" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.9" /> + </repository> + <repository changeset_revision="345685d467fb" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="matplotlib" version="1.4" /> + </repository> + <repository changeset_revision="7002d3382856" name="package_python_2_7_scipy_0_14" owner="iuc" 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" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="samtools" version="0.1.19" /> + </repository> + <repository changeset_revision="d31e73183b94" name="package_ucsc_tools_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="ucsc_tools" version="0.1" /> + </repository> + <package>https://github.com/fidelram/deepTools/archive/1.5.11.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>