Mercurial > repos > iuc > package_snpeff_3_6

comparison tool_dependencies.xml @ 1:807f8db26f0a draft default tip

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author iuc
date Wed, 18 Feb 2015 11:36:02 -0500
parents d782e523a77b
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0:d782e523a77b 1:807f8db26f0a
6 <action type="download_by_url">https://downloads.sourceforge.net/project/snpeff/snpEff_v3_6_core.zip</action> 6 <action type="download_by_url">https://downloads.sourceforge.net/project/snpeff/snpEff_v3_6_core.zip</action>
7 <action type="move_directory_files"> 7 <action type="move_directory_files">
8 <source_directory>.</source_directory> 8 <source_directory>.</source_directory>
9 <destination_directory>$INSTALL_DIR</destination_directory> 9 <destination_directory>$INSTALL_DIR</destination_directory>
10 </action> 10 </action>
11 <action type="shell_command">sed -i.orig -e 's;http://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
11 <action type="set_environment"> 12 <action type="set_environment">
12 <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> 13 <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
13 </action> 14 </action>
14 <action type="set_environment"> 15 <action type="set_environment">
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> 16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>