| Previous changeset 34:8fbd165f8835 (2013-11-04) Next changeset 36:cd98580c35e3 (2014-07-22) |
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Commit message:
Create lib directories during install, added README.txt |
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modified:
tool_dependencies.xml |
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added:
README.txt |
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| diff -r 8fbd165f8835 -r ff21a055413b README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Tue Jul 22 16:52:10 2014 -0400 |
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| @@ -0,0 +1,24 @@ +== RSeQC Galaxy Wrapper == + +This is a Galaxy wrapper for the RSeQC RNA-Seq QC package. + +** Installation ** + +Installation from a tool shed provides the necessary tool dependencies, R, numpy, and RSeQC. + +Otherwise, make sure that R and the RSeQC scripts are in the path and run under the Galaxy environment. +Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them. +Restart the Galaxy server. + +Requires Python 2.7 + +** Attribution ** + +The RSeQC package and associated documentation can be found at: http://rseqc.sourceforge.net/ + +The galaxy wrapper code was written by + Nilesh Kavthekar, School of Engineering and Applied Sciences, University of Pennsylvania, Class of 2016 +Modified by + Lance Parsons, Lewis-Sigler Institute for Integrative Genomics, Princeton University, + Björn Grüning, University of Freiburg, bjoern.gruening@gmail.com +The development of the wrapper code is housed on BitBucket at: https://bitbucket.org/lance_parsons/rseqc_galaxy_wrapper |
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| diff -r 8fbd165f8835 -r ff21a055413b tool_dependencies.xml --- a/tool_dependencies.xml Mon Nov 04 16:19:36 2013 -0500 +++ b/tool_dependencies.xml Tue Jul 22 16:52:10 2014 -0400 |
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| @@ -4,11 +4,13 @@ <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.7.1"> - <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="rseqc" version="2.3.7"> <install version="1.0"> <actions> + <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> + <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</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"> |