Mercurial > repos > crs4 > sspace
comparison tool_dependencies.xml @ 0:b1be94418db9 draft
Uploaded
| author | crs4 |
|---|---|
| date | Tue, 17 Sep 2013 09:41:18 -0400 |
| parents | |
| children | 93fa7ecb5292 |
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| -1:000000000000 | 0:b1be94418db9 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="sspace" version="2.0"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url" target_filename="SSPACE-BASIC-2.0_linux-x86_64.zip">http://www.baseclear.com/download.php?file_id=1038</action> | |
| 7 <!-- fix for Perl >= 5.16.0--> | |
| 8 <action type="shell_command">sed -i -e 's/require "getopts.pl"/use Getopt::Std/' -e 's/&Getopts/getopts/' SSPACE_Basic_v2.0.pl</action> | |
| 9 <action type="move_directory_files"> | |
| 10 <source_directory>.</source_directory> | |
| 11 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 12 </action> | |
| 13 <action type="set_environment"> | |
| 14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> | |
| 15 </action> | |
| 16 <action type="set_environment"> | |
| 17 <environment_variable name="SSPACE_SITE_OPTIONS" action="set_to">"-T 1"</environment_variable> | |
| 18 </action> | |
| 19 </actions> | |
| 20 </install> | |
| 21 <readme> | |
| 22 Change the SSPACE_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in Bowtie alignment (-T). | |
| 23 </readme> | |
| 24 </package> | |
| 25 </tool_dependency> |