Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison tool_dependencies.xml @ 79:c86f1f86b3c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yhoogstrate
date Thu, 13 Nov 2014 10:30:43 -0500
parents 398963a4827a
children c5bd139cd3e8
comparison
equal deleted inserted replaced
78:398963a4827a 79:c86f1f86b3c1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3
4 <!-- the following repo does NOT work out of the box:
5 <package name="package_r3_withx" version="3.0.1">
6 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
7 </package>
8 -->
9
10 <!-- the following repo does NOT even install due to gfortran shared libs:
11 <package name="R" version="3.1.0">
12 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
13 </package>
14 -->
15
16 <package name="R" version="3.0.3"> 3 <package name="R" version="3.0.3">
17 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> 4 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /><!-- toolshed="http://testtoolshed.g2.bx.psu.edu/" -->
18 </package> 5 </package>
19 6
20 <package name="biocLite_edgeR_limma" version="latest"> 7 <package name="biocLite_edgeR_limma" version="latest">
21 <install version="1.0"> 8 <install version="1.0">
22 <actions> 9 <actions>
23 <action type="set_environment_for_install"> 10 <action type="set_environment_for_install">
24 <!-- the following repo does NOT work out of the box: 11 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"><!-- toolshed="http://testtoolshed.g2.bx.psu.edu/" -->
25 <repository changeset_revision="abc274f22004" name="package_r3_withx" owner="joachim-jacob" toolshed="http://testtoolshed.g2.bx.psu.edu/">
26 <package name="package_r3_withx" version="3.0.1" />
27 </repository>
28 -->
29 <!-- the following repo does NOT even install due to gfortran shared libs:
30 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
31 <package name="R" version="3.1.0" />
32 </repository>
33 -->
34
35 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
36 <package name="R" version="3.0.3" /> 12 <package name="R" version="3.0.3" />
37 </repository> 13 </repository>
38 14
39 </action> 15 </action>
40 <action type="make_directory">$INSTALL_DIR</action> 16 <action type="make_directory">$INSTALL_DIR</action>
52 </readme> 28 </readme>
53 </package> 29 </package>
54 30
55 <!-- instead of using "convert", make use of "gm convert" --> 31 <!-- instead of using "convert", make use of "gm convert" -->
56 <package name="graphicsmagick" version="1.3.18"> 32 <package name="graphicsmagick" version="1.3.18">
57 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> 33 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /><!-- toolshed="http://testtoolshed.g2.bx.psu.edu/" -->
34 </package>
35
36 <package name="design_matrix_creator" version="1.0.0">
37 <install version="1.0">
38 <actions>
39 <action type="move_file">
40 <source>$REPOSITORY_INSTALL_DIR/design_matrix_creator</source>
41 <destination>$INSTALL_DIR/bin/</destination>
42 </action>
43 <action type="chmod">
44 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
45 </action>
46 <action type="set_environment">
47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
48 </action>
49 </actions>
50 </install>
58 </package> 51 </package>
59 </tool_dependency> 52 </tool_dependency>