| Previous changeset 11:f320093f1e8e (2012-12-10) Next changeset 13:30bb8acb77a4 (2013-11-05) |
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Commit message:
Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist |
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modified:
htseq-count.xml tool_dependencies.xml |
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| diff -r f320093f1e8e -r 62a1de8c8aae htseq-count.xml --- a/htseq-count.xml Mon Dec 10 13:36:54 2012 -0500 +++ b/htseq-count.xml Mon Mar 11 12:44:45 2013 -0400 |
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| @@ -1,9 +1,9 @@ -<tool id="htseq_count" name="htseq-count" version="0.3"> +<tool id="htseq_count" name="htseq-count" version="0.3.1"> <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="0.5.4p1">htseq</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.56.0">picard</requirement> </requirements> |
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| diff -r f320093f1e8e -r 62a1de8c8aae tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 10 13:36:54 2012 -0500 +++ b/tool_dependencies.xml Mon Mar 11 12:44:45 2013 -0400 |
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| @@ -16,14 +16,15 @@ </readme> </package> - <package name="htseq" version="0.5.3p9"> + <package name="htseq" version="0.5.4p1"> <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 $INSTALL_DIR/bin</action> + <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action> + <action type="make_directory">$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</environment_variable> + <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> </action> </actions> @@ -32,6 +33,7 @@ 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> @@ -55,6 +57,7 @@ Compiling SAMtools requires the ncurses and zlib development libraries. </readme> </package> + <package name="picard" version="1.56.0"> <install version="1.0"> <actions> |