| Previous changeset 3:f7a5b54a8d4f (2012-09-10) Next changeset 5:8a5d43b21c6e (2012-09-20) |
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Commit message:
Added tool_dependencies.xml back, dependency installation requires Galaxy changeset 7621:108cda898646 |
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modified:
htseq-count.xml |
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added:
tool_dependencies.xml |
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| diff -r f7a5b54a8d4f -r 14bec14f4290 htseq-count.xml --- a/htseq-count.xml Mon Sep 10 17:30:10 2012 -0400 +++ b/htseq-count.xml Tue Sep 11 17:45:23 2012 -0400 |
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| @@ -2,6 +2,7 @@ <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="0.5.3p9">htseq</requirement> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> |
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| diff -r f7a5b54a8d4f -r 14bec14f4290 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Sep 11 17:45:23 2012 -0400 |
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| @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.6.2"> + <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">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> + + <package name="htseq" version="0.5.3p9"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action> + <action type="make_directory">$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">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. + </readme> + </package> + <package name="samtools" version="0.1.18"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> + <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$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> +</tool_dependency> |