Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison tool_dependencies.xml @ 2:4895f7c6ae4d draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Sun, 21 Jun 2015 16:48:36 -0400
parents eee9701a7491
children dffa22efc6a8
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1:eee9701a7491 2:4895f7c6ae4d
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="cd2113c820f7" name="package_biocbasics" owner="mvdbeek" prior_installation_required="True" 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\",\"latticeExtra\")" &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 "install.packages(c(\"gridBase\",\"gridExtra\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
30 <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
31 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
32 </actions>
33 </install>
34 <package name="numpy" version="1.9">
35 <repository name="package_numpy_1_9" owner="iuc" prior_installation_required="True" />
36 </package>
37 <package name="scipy" version="0.14">
38 <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True" />
39 </package>
40 <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels
41 It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
42 Note we use cran at fred hutch since no fastest mirror thingy
43 </readme>
44 </package> 17 </package>
45 </tool_dependency> 18 </tool_dependency>