Mercurial > repos > drosofff > msp_sr_size_histograms

comparison tool_dependencies.xml @ 1:6c72cf9a00df draft

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Uploaded
author mvdbeek
date Sun, 29 Mar 2015 12:54:10 -0400
parents 63ff807752d7
children 9f75d887904d
comparison
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0:63ff807752d7 1:6c72cf9a00df
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">
19 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 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" /> 20 <package name="R" version="3.0.3" />
21 </repository> 21 </repository>
22 </action> 22 </action>
23 <action type="make_directory">$INSTALL_DIR</action> 23 <action type="make_directory">$INSTALL_DIR</action>
24 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action> 24 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &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> 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> 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 $INSTALL_DIR/runme.R </action> 31 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
32 </actions> 32 </actions>
33 </install> 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>
34 <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels 40 <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels
35 It's clunky but this is the most convenient way iuc could get anything installed into the package_r3 41 It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
36 Note we use cran at fred hutch since no fastest mirror thingy 42 Note we use cran at fred hutch since no fastest mirror thingy
37 </readme> 43 </readme>
38 </package> 44 </package>