Mercurial > repos > drosofff > msp_sr_signature

comparison tool_dependencies.xml @ 2:2b30861d95f4 draft

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Uploaded
author mvdbeek
date Sun, 29 Mar 2015 11:58:31 -0400
parents d613dbee3ce4
children 5c5d12cbf8ed
comparison
equal deleted inserted replaced
1:9274c7b1e85c 2:2b30861d95f4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="bowtie" version="0.12.7"> 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" /> 4 <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="samtools" version="0.1.18"> 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" /> 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="240d1ad9f207" 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="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" /> 13 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" 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 <install version="1.0">
17 <actions> 17 <actions>
18 <action type="set_environment_for_install"> 18 <action type="set_environment_for_install">
28 <action type="shell_command">echo "biocLite(installme)" &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> 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 $INSTALL_DIR/runme.R </action> 30 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
31 </actions> 31 </actions>
32 </install> 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>
33 <readme>Installs some basic bioc packages for the lattice wrapper for managing lattice panels 39 <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 40 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 41 Note we use cran at fred hutch since no fastest mirror thingy
36 </readme> 42 </readme>
37 </package> 43 </package>