|
61
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
76
|
3 <package name="ghostscript" version="9.07">
|
|
|
4 <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
|
|
61
|
5 </package>
|
|
|
6 <package name="graphicsmagick" version="1.3.18">
|
|
|
7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
|
|
|
8 </package>
|
|
91
|
9 <package name="r303" version="3.0.3">
|
|
|
10 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
|
|
|
11 </package>
|
|
61
|
12 <package name="biocbasics" version="2.14">
|
|
|
13 <install version="1.0">
|
|
|
14 <actions>
|
|
|
15 <action type="set_environment_for_install">
|
|
91
|
16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
|
|
87
|
17 <package name="r303" version="3.0.3" />
|
|
61
|
18 </repository>
|
|
|
19 </action>
|
|
97
|
20 <action type="make_directory">$INSTALL_DIR</action>
|
|
|
21 <action type="move_file">
|
|
101
|
22 <source>runme.R</source>
|
|
97
|
23 <destination>$INSTALL_DIR</destination>
|
|
|
24 </action>
|
|
|
25 <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action>
|
|
61
|
26 </actions>
|
|
|
27 </install>
|
|
|
28 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
|
|
|
29 It's clunky but this is the most convenient way I could get anything installed into the package_r3
|
|
|
30 Note we use cran at fred hutch since no fastest mirror thingy
|
|
|
31 If atlas will not compile - eg: it thinks autoscaling is on or something,
|
|
|
32 you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references
|
|
|
33 </readme>
|
|
|
34 </package>
|
|
|
35 </tool_dependency>
|
