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comparison tool_dependencies.xml @ 0:d44a316336e5 draft

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author iuc
date Thu, 08 Jan 2015 11:41:43 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="squid" version="1.9g">
4 <repository changeset_revision="b83db9c73d4b" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="randfold" version="2.0">
7 <install version="1.0">
8 <actions>
9 <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
10 <action type="set_environment_for_install">
11 <repository changeset_revision="b83db9c73d4b" name="package_squid_1_9g" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
12 <package name="squid" version="1.9g" />
13 </repository>
14 </action>
15 <action type="shell_command">make</action>
16 <action type="move_file">
17 <source>randfold</source>
18 <destination>$INSTALL_DIR/bin</destination>
19 </action>
20 <action type="set_environment">
21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
22 </action>
23 </actions>
24 </install>
25 <readme>
26
27 RANDFOLD - A randsomization test for sequence secondary structure
28 Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB
29 -----------------------------------------------------------------------------
30
31 This is RANDFOLD version 2. The software compute the probability that, for a
32 given sequence, the Minimum Free Energy (MFE) of the secondary structure is
33 different from MFE computed with random sequences.
34
35 For more information, see the paper published in Bioinformatics:
36
37 Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
38 Evidence that microRNA precursors, unlike other non-coding RNAs, have lower
39 folding free energies than random sequences.
40 Bioinformatics. 2004 Nov 22;20(17):2911-7.
41 PMID: 15217813
42
43 </readme>
44 </package>
45 </tool_dependency>