comparison tool_dependencies.xml @ 1:53e370639b89 draft default tip

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0:b34d2c942c79

<?xml version="1.0"?>
<tool_dependency>
  <package name="squid" version="1.9g">
      <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="randfold" version="2.0">
      <install version="1.0">
          <actions>
              <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
                <action type="set_environment_for_install">
                  <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                      <package name="squid" version="1.9g" />
                    </repository>
                </action>
                <action type="shell_command">make</action>
                <action type="move_file">
                  <source>randfold</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

RANDFOLD - A randsomization test for sequence secondary structure 
Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB
-----------------------------------------------------------------------------

This is RANDFOLD version 2. The software compute the probability that, for a 
given sequence, the Minimum Free Energy (MFE) of the secondary structure is 
different from MFE computed with random sequences. 

For more information, see the paper published in Bioinformatics:

Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower 
folding free energies than random sequences.
Bioinformatics. 2004 Nov 22;20(17):2911-7.
PMID: 15217813

        </readme>

1:53e370639b89

<?xml version="1.0"?>
<tool_dependency>
    <package name="squid" version="1.9g">
        <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="randfold" version="2.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="squid" version="1.9g" />
                    </repository>
                </action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>randfold</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

RANDFOLD - A randsomization test for sequence secondary structure
Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB
-----------------------------------------------------------------------------

This is RANDFOLD version 2. The software compute the probability that, for a
given sequence, the Minimum Free Energy (MFE) of the secondary structure is
different from MFE computed with random sequences.

For more information, see the paper published in Bioinformatics:

Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower
folding free energies than random sequences.
Bioinformatics. 2004 Nov 22;20(17):2911-7.
PMID: 15217813

        </readme>