Mercurial > repos > drosofff > msp_sr_signature

comparison tool_dependencies.xml @ 7:46405fd09d06 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Sun, 21 Jun 2015 16:04:56 -0400
parents 5c5d12cbf8ed
children 4c546f1e6fa2
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6:d2a220e64a1c 7:46405fd09d06
7 <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="pysam" version="0.7.7"> 9 <package name="pysam" version="0.7.7">
10 <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="R" version="3.0.3"> 12 <package name="numpy" version="1.9">
13 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="biocbasics" version="2.14"> 15 <package name="biocbasics" version="2.14">
16 <install version="1.0"> 16 <repository changeset_revision="1028c26e63c8" name="package_biocbasics" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 <actions>
18 <action type="set_environment_for_install">
19 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
20 <package name="R" version="3.0.3" />
21 </repository>
22 </action>
23 <action type="make_directory">$INSTALL_DIR</action>
24 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
25 <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
26 <action type="shell_command">echo "installme=c(\"lattice\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
27 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
28 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
29 <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
30 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
31 </actions>
32 </install>
33 <package name="numpy" version="1.9">
34 <repository name="package_numpy_1_9" owner="iuc" prior_installation_required="True" />
35 </package>
36 <package name="scipy" version="0.14">
37 <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True" />
38 </package>
39 <readme>Installs some basic bioc packages for the lattice wrapper for managing lattice panels
40 It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
41 Note we use cran at fred hutch since no fastest mirror thingy
42 </readme>
43 </package> 17 </package>
44 </tool_dependency> 18 </tool_dependency>