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comparison tool_dependencies.xml @ 0:8a8adbf98ecc draft

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author iuc
date Fri, 16 May 2014 07:57:33 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="bowtie2" version="2.1.0">
4 <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="fastq_screen" version="0.4.2">
7 <install version="1.0">
8 <actions>
9 <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.4.2.tar.gz</action>
10 <action type="move_directory_files">
11 <source_directory>.</source_directory>
12 <destination_directory>$INSTALL_DIR</destination_directory>
13 </action>
14 <action type="set_environment">
15 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
16 </action>
17 </actions>
18 </install>
19 <readme>
20 Galaxy wrapper for http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ from Simon Andrews.
21 Useful if you want to (eg) check your RNA sequence from a cell culture for contamination from (eg) Mycoplasma Genitalium, or if you have sequence from an unknown organism :(
22 Permanently set to use your Galaxy bowtie2 indices - expects Bowtie2 to be installed so the Galaxy package_bowtie2 is installed if it's not already there.
23
24 ###WARNING### The fastq_screen perl script requires that the GD::Graph http://search.cpan.org/~bwarfield/GDGraph/Graph.pm module be installed.
25 Otherwise, NO plot will be created. This wrapper relies on the system perl - a proper Galaxy perl dependency is just too icky to think about.
26
27 Send code if you think otherwise.
28 </readme>
29 </package>
30
31 </tool_dependency>