Mercurial > repos > yhoogstrate > featurecounts
view tool_dependencies.xml @ 6:fae19d64e9de draft
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author | yhoogstrate |
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date | Thu, 13 Nov 2014 09:46:22 -0500 |
parents | 9fcffbe6c206 |
children | 2312bedfe2a3 |
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<?xml version="1.0"?> <tool_dependency> <package name="featurecounts" version="1.4.4"> <install version="1.0"> <actions> <action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz && tar -zxvf subread-1.4.4-source.tar.gz && cd subread-1.4.4-source/src/ && make -f Makefile.Linux && cd ../../</action> <action type="move_file"> <source>../subread-1.4.4-source/bin/featureCounts</source> <destination>$INSTALL_DIR/bin/</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>--> </action> </actions> </install> <readme> Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed. </readme> </package> <package name="featurecounts2bed" version="1.0.0"> <install version="1.0"> <actions> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/featurecounts2bed.sh</source> <destination>$INSTALL_DIR/bin/</destination> </action> <!-- Revert to the previous if the move command doesn't work <action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh && chmod 755 *.sh</action> <action type="move_file"> <source>../featurecounts2bed.sh</source> <destination>$INSTALL_DIR/bin</destination> </action> --> <action type="chmod"> <file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> </tool_dependency>