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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="squid" version="1.9g">
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4 <repository changeset_revision="8ebcef4aedfb" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="randfold" version="2.0">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
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10 <action type="set_environment_for_install">
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2
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11 <repository changeset_revision="8ebcef4aedfb" name="package_squid_1_9g" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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12 <package name="squid" version="1.9g" />
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13 </repository>
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14 </action>
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15 <action type="shell_command">make</action>
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16 <action type="move_file">
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17 <source>randfold</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>
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26
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27 RANDFOLD - A randsomization test for sequence secondary structure
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28 Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp; Evolutionary Genomics - VIB
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29 -----------------------------------------------------------------------------
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30
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31 This is RANDFOLD version 2. The software compute the probability that, for a
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32 given sequence, the Minimum Free Energy (MFE) of the secondary structure is
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33 different from MFE computed with random sequences.
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34
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35 For more information, see the paper published in Bioinformatics:
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36
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37 Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
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38 Evidence that microRNA precursors, unlike other non-coding RNAs, have lower
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39 folding free energies than random sequences.
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40 Bioinformatics. 2004 Nov 22;20(17):2911-7.
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41 PMID: 15217813
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42
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43 </readme>
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44 </package>
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45 </tool_dependency>
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