Mercurial > repos > rnateam > mirdeep2_mapper

comparison tool_dependencies.xml @ 1:12fc62b7dc09 draft

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Uploaded
author rnateam
date Thu, 12 Feb 2015 09:46:55 -0500
parents af18bb0baa92
children ab8cd78709e1
comparison
equal deleted inserted replaced
0:af18bb0baa92 1:12fc62b7dc09
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="perl" version="5.18.1"> 3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="bowtie" version="0.12.7"> 6 <package name="bowtie" version="0.12.7">
7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="mirdeep2_mapper" version="2.0"> 9 <package name="mirdeep2_mapper" version="2.0">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions> 11 <actions>
12 <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action> 12 <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
13 <action type="move_file"> 13 <action type="move_file">
14 <source>clip_adapters.pl</source> 14 <source>clip_adapters.pl</source>
15 <destination>$INSTALL_DIR</destination> 15 <destination>$INSTALL_DIR</destination>
16 </action> 16 </action>
17 <action type="move_file"> 17 <action type="move_file">
18 <source>collapse_reads_md.pl</source> 18 <source>collapse_reads_md.pl</source>
19 <destination>$INSTALL_DIR</destination> 19 <destination>$INSTALL_DIR</destination>
20 </action> 20 </action>
21 <action type="move_file"> 21 <action type="move_file">
22 <source>convert_bowtie_output.pl</source> 22 <source>convert_bowtie_output.pl</source>
23 <destination>$INSTALL_DIR</destination> 23 <destination>$INSTALL_DIR</destination>
24 </action> 24 </action>
25 <action type="move_file"> 25 <action type="move_file">
26 <source>fastaparse.pl</source> 26 <source>fastaparse.pl</source>
27 <destination>$INSTALL_DIR</destination> 27 <destination>$INSTALL_DIR</destination>
28 </action> 28 </action>
29 <action type="move_file"> 29 <action type="move_file">
30 <source>fastq2fasta.pl</source> 30 <source>fastq2fasta.pl</source>
31 <destination>$INSTALL_DIR</destination> 31 <destination>$INSTALL_DIR</destination>
32 </action> 32 </action>
33 <action type="move_file"> 33 <action type="move_file">
34 <source>illumina_to_fasta.pl</source> 34 <source>illumina_to_fasta.pl</source>
35 <destination>$INSTALL_DIR</destination> 35 <destination>$INSTALL_DIR</destination>
36 </action> 36 </action>
37 <action type="move_file"> 37 <action type="move_file">
38 <source>mapper.pl</source> 38 <source>mapper.pl</source>
39 <destination>$INSTALL_DIR</destination> 39 <destination>$INSTALL_DIR</destination>
40 </action> 40 </action>
41 <action type="move_file"> 41 <action type="move_file">
42 <source>parse_mappings.pl</source> 42 <source>parse_mappings.pl</source>
43 <destination>$INSTALL_DIR</destination> 43 <destination>$INSTALL_DIR</destination>
44 </action> 44 </action>
45 <action type="move_file"> 45 <action type="move_file">
46 <source>rna2dna.pl</source> 46 <source>rna2dna.pl</source>
47 <destination>$INSTALL_DIR</destination> 47 <destination>$INSTALL_DIR</destination>
48 </action> 48 </action>
49 <action type="set_environment"> 49 <action type="set_environment">
50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> 50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
51 </action> 51 </action>
52 </actions> 52 </actions>
53 </install> 53 </install>
54 <readme> 54 <readme>
55 55