Mercurial > repos > bgruening > deeptools_bam_coverage
changeset 18:07187f021c89 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356
| author | bgruening |
|---|---|
| date | Fri, 18 Mar 2016 08:33:28 -0400 |
| parents | 0e335fe39725 |
| children | 205f1536914d |
| files | deepTools_macros.xml tool_dependencies.xml tool_dependencies.xml.orig |
| diffstat | 3 files changed, 3 insertions(+), 79 deletions(-) [+] |
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--- a/deepTools_macros.xml Thu Mar 10 02:49:48 2016 -0500 +++ b/deepTools_macros.xml Fri Mar 18 08:33:28 2016 -0400 @@ -340,7 +340,7 @@ ln -s "${bamfile}" "./${counter}.bam" && ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && #silent $files.append('%s.bam' % $counter) - #silent $labels.append('%s' % ($bamfile.display_name)) + #silent $labels.append("'%s'" % ($bamfile.display_name)) #end for ]]> </token> @@ -352,7 +352,7 @@ #for $counter, $bigwig in enumerate($bigwigfiles): ln -s "${bigwig}" "${counter}.bw" && #silent $files.append('%s.bw' % $counter) - #silent $labels.append('%s' % ($bigwig.display_name)) + #silent $labels.append("'%s'" % ($bigwig.display_name)) #end for ]]> </token>
--- a/tool_dependencies.xml Thu Mar 10 02:49:48 2016 -0500 +++ b/tool_dependencies.xml Fri Mar 18 08:33:28 2016 -0400 @@ -4,6 +4,6 @@ <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deepTools" version="2.2.2"> - <repository changeset_revision="cc55b7267451" name="package_python_2_7_deeptools_2_2_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="461a47fb8582" name="package_python_2_7_deeptools_2_2_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
--- a/tool_dependencies.xml.orig Thu Mar 10 02:49:48 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -<?xml version='1.0' encoding='utf-8'?> -<tool_dependency> - <package name="numpy" version="1.9"> - <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" /> - </package> - <package name="pybigwig" version="0.2.4"> - <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc" prior_installation_required="True"/> - </package> - <package name="matplotlib" version="1.4"> - <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" /> - </package> - <package name="scipy" version="0.14"> - <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" /> - </package> -<<<<<<< HEAD - <package name="deepTools" version="2.0.1"> - <repository name="package_python_2_7_deeptools_2_0_1" owner="iuc"/> -======= - <package name="pysam" version="0.8.3"> - <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" /> - </package> - <package name="bx-python" version="0.7.2"> - <repository name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" /> - </package> - <package name="python" version="2.7.10"> - <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" /> ->>>>>>> d56067f86089e75354a2fad266002db3730766d9 - </package> - <package name="deepTools" version="2.1.0"> - <install version="1.0"> - <actions> - <action type="setup_python_environment"> - <repository name="package_python_2_7_10" owner="iuc"> - <package name="python" version="2.7.10" /> - </repository> - <repository name="package_python_2_7_pysam_0_8_3" owner="iuc"> - <package name="pysam" version="0.8.3" /> - </repository> - <repository name="package_python_2_7_numpy_1_9" owner="iuc"> - <package name="numpy" version="1.9" /> - </repository> - <repository name="package_python_2_7_matplotlib_1_4" owner="iuc"> - <package name="matplotlib" version="1.4" /> - </repository> - <repository name="package_python_2_7_scipy_0_14" owner="iuc"> - <package name="scipy" version="0.14" /> - </repository> - <repository name="package_python_2_7_bx_python_0_7" owner="iuc"> - <package name="bx-python" version="0.7.2" /> - </repository> - <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc"> - <package name="pybigwig" version="0.2.4" /> - </repository> - <package sha256sum="3bf835afde02cd5247198db3e01f690899e1fdb86e1821a83ac940d807baa857">https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz</package> - </action> - - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable> - <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> - <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable> - <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> - <!-- libpng lib path --> - <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable> - <!-- disable the config file of deepTools --> - <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable> - </action> - </actions> - </install> - <readme> - Installation of deepTools from Fidel Ramirez. - https://github.com/fidelram/deepTools - </readme> - </package> -</tool_dependency>