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comparison FastQC/tool_dependencies.xml @ 2:45cd27a2ad5c draft

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Fix for installing fastqc zip - control zip to unzip into final resting place
author fubar
date Mon, 03 Jun 2013 21:46:21 -0400
parents 42251cbdeeac
children 0bec27668020
comparison
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1:91cb2603b56c 2:45cd27a2ad5c
4 <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/jars/FastQC</environment_variable> 4 <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/jars/FastQC</environment_variable>
5 </set_environment> 5 </set_environment>
6 <package name="FastQC" version="0.10.1"> 6 <package name="FastQC" version="0.10.1">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action> 9 <action type="download_file">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
10 <action type="move_directory_files"> 10 <action type="shell_command">unzip fastqc_v0.10.1.zip -d $INSTALL_DIR/jars/FastQC</action>
11 <source_directory>FastQC</source_directory>
12 <destination_directory>$INSTALL_DIR/jars</destination_directory>
13 </action>
14 <action type="shell_command">chmod ugo+x $INSTALL_DIR/jars/FastQC/fastqc</action> 11 <action type="shell_command">chmod ugo+x $INSTALL_DIR/jars/FastQC/fastqc</action>
15 </actions> 12 </actions>
16 </install> 13 </install>
17 <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment 14 <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment
18 available to all potential execution nodes for this tool to work. 15 available to all potential execution nodes for this tool to work.