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comparison tool_dependencies.xml @ 0:d613dbee3ce4

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Imported from capsule None
author drosofff
date Mon, 03 Nov 2014 10:29:28 -0500
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children 2b30861d95f4
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-1:000000000000 0:d613dbee3ce4
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="bowtie" version="0.12.7">
4 <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="samtools" version="0.1.18">
7 <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="pysam" version="0.7.7">
10 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="R" version="3.0.3">
13 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="biocbasics" version="2.14">
16 <install version="1.0">
17 <actions>
18 <action type="set_environment_for_install">
19 <repository changeset_revision="9ff23e0b280b" 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 <readme>Installs some basic bioc packages for the lattice wrapper for managing lattice panels
34 It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
35 Note we use cran at fred hutch since no fastest mirror thingy
36 </readme>
37 </package>
38 </tool_dependency>