Mercurial > repos > iuc > package_randfold_2_0

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author iuc
date Wed, 04 Feb 2015 13:19:09 -0500
parents b34d2c942c79
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0:b34d2c942c79 1:53e370639b89
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="squid" version="1.9g"> 3 <package name="squid" version="1.9g">
4 <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="randfold" version="2.0"> 6 <package name="randfold" version="2.0">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action> 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"> 10 <action type="set_environment_for_install">
11 <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 11 <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
12 <package name="squid" version="1.9g" /> 12 <package name="squid" version="1.9g" />
13 </repository> 13 </repository>
14 </action> 14 </action>
15 <action type="shell_command">make</action> 15 <action type="shell_command">make</action>
16 <action type="move_file"> 16 <action type="move_file">
17 <source>randfold</source> 17 <source>randfold</source>
18 <destination>$INSTALL_DIR/bin</destination> 18 <destination>$INSTALL_DIR/bin</destination>
19 </action> 19 </action>
20 <action type="set_environment"> 20 <action type="set_environment">
21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
22 </action> 22 </action>
23 </actions> 23 </actions>
24 </install> 24 </install>
25 <readme> 25 <readme>
26 26
27 RANDFOLD - A randsomization test for sequence secondary structure 27 RANDFOLD - A randsomization test for sequence secondary structure
28 Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB 28 Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB
29 ----------------------------------------------------------------------------- 29 -----------------------------------------------------------------------------
30 30
31 This is RANDFOLD version 2. The software compute the probability that, for a 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 32 given sequence, the Minimum Free Energy (MFE) of the secondary structure is
33 different from MFE computed with random sequences. 33 different from MFE computed with random sequences.
34 34
35 For more information, see the paper published in Bioinformatics: 35 For more information, see the paper published in Bioinformatics:
36 36
37 Bonnet E, Wuyts J, Rouze P, Van de Peer Y. 37 Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
38 Evidence that microRNA precursors, unlike other non-coding RNAs, have lower 38 Evidence that microRNA precursors, unlike other non-coding RNAs, have lower
39 folding free energies than random sequences. 39 folding free energies than random sequences.
40 Bioinformatics. 2004 Nov 22;20(17):2911-7. 40 Bioinformatics. 2004 Nov 22;20(17):2911-7.
41 PMID: 15217813 41 PMID: 15217813
42 42
43 </readme> 43 </readme>