Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_10
changeset 0:6a8a27d4992b 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 15:01:25 -0400 |
| parents | |
| children | fde32464913e |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 93 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun May 17 15:01:25 2015 -0400 @@ -0,0 +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="a095a5975d3a" 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" /> + </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" /> + </package> + <package name="bx-python" version="0.7.2"> + <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> + <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="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="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"> + <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"> + <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> + </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>