# HG changeset patch # User lparsons # Date 1383674563 18000 # Node ID 30bb8acb77a4ea09b5a1166de04e437babb4f29d # Parent 62a1de8c8aae22a529b3d5bda3bb64dad20ee482 Updated to v0.5.4p5, use repository dependencies. diff -r 62a1de8c8aae -r 30bb8acb77a4 .hgignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Tue Nov 05 13:02:43 2013 -0500 @@ -0,0 +1,3 @@ +^package$ +syntax: glob +*.pyc diff -r 62a1de8c8aae -r 30bb8acb77a4 .hgtags --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgtags Tue Nov 05 13:02:43 2013 -0500 @@ -0,0 +1,3 @@ +142ec9462fa644cd29642ea0ad10e9889ce75619 0.3 +3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2 +496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1 diff -r 62a1de8c8aae -r 30bb8acb77a4 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Nov 05 13:02:43 2013 -0500 @@ -0,0 +1,51 @@ +htseq-count wrapper for Galaxy +============================== + +Galaxy wrapper for +[htseq-count](http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) +script from python +[HTSeq](http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) package. + +Installation +------------ + +Installtion directly from the [Galaxy +Toolshed](http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) is +recommended. + +Development +----------- + +Repository-Maintainer: Lance Parsons + +Repository-Development: + + +License +------- + +Copyright (c) 2012-2013, Lance R. Parsons +All rights reserved. + +Licensed under the BSD 2-Clause License: + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff -r 62a1de8c8aae -r 30bb8acb77a4 fabfile.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fabfile.py Tue Nov 05 13:02:43 2013 -0500 @@ -0,0 +1,26 @@ +from fabric.api import local +from fabric.operations import prompt +import os + + +def package(): + ''' + Pacakge for upload to toolshed + packaging 'test' version (default) uses local directory + otherwise, specify a mercurial tag to package + ''' + package_dir = 'package' + base_filename = os.path.join(package_dir, 'htseq-count') + version = prompt("Enter version number for package [test]:") + revision_option = '' + if version != '': + revision_option = '-r "%s"' % version + else: + version = 'test' + version_filename = '%s_%s.tar.gz' % (base_filename, version) + local('mkdir -p %s' % package_dir) + local('rm -f %s' % version_filename) + if version == 'test': + local('tar czvf %s --exclude "fabfile.*" --exclude "%s" --exclude ".hg*" *' % (version_filename, package_dir)) + else: + local('hg archive -t tgz %s -X "fabfile.*" -X "package" -X ".hg*" -p . "%s"' % (revision_option, version_filename)) diff -r 62a1de8c8aae -r 30bb8acb77a4 htseq-count.xml --- a/htseq-count.xml Mon Mar 11 12:44:45 2013 -0400 +++ b/htseq-count.xml Tue Nov 05 13:02:43 2013 -0500 @@ -1,10 +1,10 @@ - + - Count aligned reads in a BAM file that overlap features in a GFF file htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/' - numpy - htseq - samtools + numpy + htseq + samtools picard @@ -188,7 +188,7 @@ The following figure illustrates the effect of these three modes: -.. image:: /static/images/count_modes.png +.. image:: $PATH_TO_IMAGES/count_modes.png :width: 500 diff -r 62a1de8c8aae -r 30bb8acb77a4 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 11 12:44:45 2013 -0400 +++ b/tool_dependencies.xml Tue Nov 05 13:02:43 2013 -0500 @@ -1,31 +1,34 @@ - + + + + + + + + + + + + + + - http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz - $INSTALL_DIR/lib/python - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin - - $INSTALL_DIR/lib/python - $INSTALL_DIR/bin + https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz + + + + + - - - - - - - - - - https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz $INSTALL_DIR/lib/python $INSTALL_DIR/lib64/python export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin - $INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python - $INSTALL_DIR/bin + $INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python + $INSTALL_DIR/bin @@ -34,44 +37,4 @@ - - - - http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2 - sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile - make - - samtools - $INSTALL_DIR/bin - - - misc/maq2sam-long - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - - - - Compiling SAMtools requires the ncurses and zlib development libraries. - - - - - - - http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip - - picard-tools-1.56 - $INSTALL_DIR/jars - - - $INSTALL_DIR/jars - - - - - -