Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison tool_dependencies.xml @ 1:a4a4c88783ea draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
author yhoogstrate
date Tue, 01 Sep 2015 04:59:05 -0400
parents acb56603b268
children ec951a5017f8
comparison
equal deleted inserted replaced
0:acb56603b268 1:a4a4c88783ea
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R" version="3.0.3"> 3 <package name="edger" version="3.11.0">
4 <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="8b2965eeb34e" name="package_r_edger_3_11_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 6
7 <package name="biocLite_edgeR_limma" version="latest"> 7 <package name="design_matrix_creator" version="1.0.0">
8 <install version="1.0"> 8 <install version="1.0">
9 <actions> 9 <actions>
10 <action type="set_environment_for_install"> 10 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/design_matrix_creator $INSTALL_DIR/bin/</action>
11 <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 11 <action type="chmod">
12 <package name="R" version="3.0.3" /> 12 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
13 </repository> 13 </action>
14 14 <action type="set_environment">
15 </action> 15 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
16 <action type="make_directory">$INSTALL_DIR</action> 16 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
17 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action> 17 </action>
18 <action type="shell_command">echo "installme=c('edgeR','limma')" &gt;&gt; $INSTALL_DIR/runme.R</action> 18 </actions>
19 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action> 19 </install>
20 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action> 20 </package>
21 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action> 21
22 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action> 22 <package name="edger_dge_table_to_bedgraph" version="1.0.0">
23 <action type="shell_command">export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action> 23 <install version="1.0">
24 </actions> 24 <actions>
25 </install> 25 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action>
26 <readme> 26 <action type="chmod">
27 Installs the latest bioc packages: edgeR &amp; Limma 27 <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file>
28 </readme> 28 </action>
29 </package> 29 <action type="set_environment">
30 30 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
31 <package name="design_matrix_creator" version="1.0.0"> 31 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
32 <install version="1.0"> 32 </action>
33 <actions> 33 </actions>
34 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action> 34 </install>
35 <action type="chmod"> 35 </package>
36 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
37 </action>
38 <action type="set_environment">
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
40 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
41 </action>
42 </actions>
43 </install>
44 </package>
45
46 <package name="edger_dge_table_to_bedgraph" version="1.0.0">
47 <install version="1.0">
48 <actions>
49 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action>
50 <action type="chmod">
51 <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file>
52 </action>
53 <action type="set_environment">
54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
55 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
56 </action>
57 </actions>
58 </install>
59 </package>
60 </tool_dependency> 36 </tool_dependency>