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comparison tool_dependencies.xml @ 2:bc4451edb703 draft

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Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
author crs4
date Mon, 27 Oct 2014 14:11:57 -0400
parents 93fa7ecb5292
children
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1:93fa7ecb5292 2:bc4451edb703
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sspace" version="2.0"> 3 <package name="bowtie" version="1.0.0">
4 <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="sspace" version="2.1">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <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> 9 <action target_filename="sspace_basic-2.1.tar.gz" type="download_by_url">https://github.com/nsoranzo/sspace_basic/archive/v2.1.tar.gz</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/&amp;Getopts/getopts/' SSPACE_Basic_v2.0.pl</action>
9 <action type="move_directory_files"> 10 <action type="move_directory_files">
10 <source_directory>.</source_directory> 11 <source_directory>.</source_directory>
11 <destination_directory>$INSTALL_DIR</destination_directory> 12 <destination_directory>$INSTALL_DIR</destination_directory>
12 </action> 13 </action>
13 <action type="set_environment"> 14 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> 15 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
15 </action> 16 </action>
16 </actions> 17 </actions>
17 </install> 18 </install>
18 <readme> 19 <readme>
19 Configuration: Previously (until Release 0), the SSPACE_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use in Bowtie alignment (-T). This is not used anymore and may be removed. 20 Configuration: Previously (until Release 0), the SSPACE_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use in Bowtie alignment (-T). This is not used anymore and may be removed.