Mercurial > repos > stemcellcommons > macs2
changeset 17:e047d7bbace9
Remove MACS2 external dependency. Change tool name and version number.
| author | Ilya Sytchev <isytchev@hsph.harvard.edu> |
|---|---|
| date | Tue, 15 Oct 2013 16:33:52 -0400 |
| parents | 14f378e35191 |
| children | 9578bc265c59 |
| files | macs2_wrapper.xml tool_dependencies.xml |
| diffstat | 2 files changed, 2 insertions(+), 43 deletions(-) [+] |
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--- a/macs2_wrapper.xml Fri Jan 25 11:49:55 2013 -0500 +++ b/macs2_wrapper.xml Tue Oct 15 16:33:52 2013 -0400 @@ -1,9 +1,4 @@ -<tool id="modencode_peakcalling_macs2" name="MACS2" version="2.0.10.2"> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <!--<requirement type="set_environment">SCRIPT_PATH</requirement>--> - </requirements> +<tool id="macs2_peakcalling" name="MACS2" version="2.0.10"> <description>Model-based Analysis of ChIP-Seq</description> <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command> <inputs> @@ -230,4 +225,4 @@ Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. </help> -</tool> \ No newline at end of file +</tool>
--- a/tool_dependencies.xml Fri Jan 25 11:49:55 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="macs2" version="2.0.10.2"> - <install version="1.0"> - <!--<actions> - <action type="download_by_url">http://data.modencode.org/modENCODE_Galaxy/tarballs/Python-2.7.3.tar.bz2</action> - <action type="shell_command">./configure</action> - <action type="shell_command">make -j</action> - <action type="shell_command">sudo -n make install</action> - <action type="shell_command">sudo -n chmod ag+w /usr/local/lib/python2.7/site-packages</action> - <action type="shell_command">sudo -n chmod ag+wx /usr/local/bin</action> - </actions>--> - <actions> - <action type="download_by_url">http://data.modencode.org/modENCODE_Galaxy/tarballs/macs2pkg.tar</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="move_directory_files"> - <source_directory>lib</source_directory> - <destination_directory>$INSTALL_DIR/lib</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable> - </action> - </actions> - </install> - <readme>Macs2 depends on having python2.7 installed on all nodes of the work cluster</readme> - </package> -</tool_dependency> - -<!--<action type="download_by_url">http://data.modencode.org/modENCODE_Galaxy/tarballs/numpy.tar</action> - <action type="shell_command">sudo -n python setup.py build</action> - <action type="shell_command">sudo -n python setup.py install</action>--> -