Mercurial > repos > lparsons > htseq_count
diff tool_dependencies.xml @ 13:30bb8acb77a4
Updated to v0.5.4p5, use repository dependencies.
author | lparsons |
---|---|
date | Tue, 05 Nov 2013 13:02:43 -0500 |
parents | 62a1de8c8aae |
children | 265ca0f35789 |
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--- 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 @@ <?xml version="1.0"?> <tool_dependency> - <package name="numpy" version="1.6.2"> + + <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" /> + </package> + + <package name="samtools" version="0.1.19"> + <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="picard" version="1.56.0"> + <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.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">$INSTALL_DIR/bin</environment_variable> + <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action> + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.7.1" /> + </repository> </action> - </actions> - </install> - <readme> - </readme> - </package> - - <package name="htseq" version="0.5.4p1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action> <action type="make_directory">$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">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> @@ -34,44 +37,4 @@ </readme> </package> - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$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>