Mercurial > repos > jeremie > package_pindel_0_2_5
view tool_dependencies.xml @ 27:ae37c0fd6590 draft default tip
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author | jeremie |
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date | Fri, 20 Jun 2014 10:40:33 -0400 |
parents | 47817c968422 |
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<?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.18"> <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True" /> </package> <package name="pindel" version="0.2.5"> <install version="1.0"> <actions> <!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> --> <action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action> <action type="shell_command">ls ..</action> <action type="shell_command"> echo "$samtools samtools $PATH $INSTALL_DIR" </action> <!-- <action type="shell_command">ls</action> --> <!-- <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="shell_command">unzip pindel-master.zip -d pindel</action> <action type="shell_command">cd master</action> --> <!-- <action type="shell_command">sed '50d' Makefile</action> --> <!-- <action type="shell_command">make Makefile.local</action> --> <action type="shell_command"> echo "SAMTOOLS= THREADS= COLOUSINGBD15_TIME=60 COLOWOBD15_TIME=80 SIM1CHRVS20305_TIME=60" > Makefile.local </action> <action type="shell_command">make SAMTOOLS=samtools THREADS=2</action> <action type="move_file"> <source>pindel</source> <destination>$INSTALL_DIR/</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> </readme> </package> </tool_dependency>