Mercurial > repos > lparsons > htseq_count
changeset 8:65c91537862c
Updated to HTSeq 0.5.4p5, use tool shed repository dependencies
| author | lparsons |
|---|---|
| date | Mon, 04 Nov 2013 16:24:18 -0500 |
| parents | 1615d0b5b809 |
| children | 4b38d1c94981 |
| files | .hgignore .hgtags fabfile.py htseq-count.xml test-data/._htseq-test-paired_counts.tsv test-data/._htseq-test-paired_othercounts.tsv tool_dependencies.xml |
| diffstat | 7 files changed, 54 insertions(+), 65 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Mon Nov 04 16:24:18 2013 -0500 @@ -0,0 +1,3 @@ +^package$ +syntax: glob +*.pyc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgtags Mon Nov 04 16:24:18 2013 -0500 @@ -0,0 +1,3 @@ +142ec9462fa644cd29642ea0ad10e9889ce75619 0.3 +3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2 +496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fabfile.py Mon Nov 04 16:24:18 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))
--- a/htseq-count.xml Fri Mar 22 13:40:24 2013 -0400 +++ b/htseq-count.xml Mon Nov 04 16:24:18 2013 -0500 @@ -1,10 +1,10 @@ -<tool id="htseq_count" name="htseq-count" version="0.3.1"> +<tool id="htseq_count" name="htseq-count" version="0.3.2"> <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> <requirements> - <requirement type="package" version="1.6.2">numpy</requirement> - <requirement type="package" version="0.5.4p1">htseq</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="0.5.4p5">htseq</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="1.56.0">picard</requirement> </requirements> <command> @@ -188,7 +188,7 @@ The following figure illustrates the effect of these three modes: -.. image:: ./static/images/count_modes.png +.. image:: $PATH_TO_IMAGES/count_modes.png :width: 500
--- a/tool_dependencies.xml Fri Mar 22 13:40:24 2013 -0400 +++ b/tool_dependencies.xml Mon Nov 04 16:24:18 2013 -0500 @@ -1,31 +1,28 @@ <?xml version="1.0"?> <tool_dependency> - <package name="numpy" version="1.6.2"> + + <package name="numpy" version="1.7.1"> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools" version="1.1.19"> + <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="picard" version="1.56.0"> + <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="htseq" version="0.5.4p5"> <install version="1.0"> <actions> - <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> - <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> - - <package name="htseq" version="0.5.4p1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action> + <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> @@ -34,44 +31,4 @@ </readme> </package> - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> - </package> - - <package name="picard" version="1.56.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action> - <action type="move_directory_files"> - <source_directory>picard-tools-1.56</source_directory> - <destination_directory>$INSTALL_DIR/jars</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> </tool_dependency>