Mercurial > repos > iuc > package_r_3_0_1_with_atlas

annotate tool_dependencies.xml @ 0:4aa16d4746cb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 15:01:02 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
2 <tool_dependency>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
3 <package name="atlas" version="3.10.1">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
4 <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
5 </package>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
6 <package name="readline" version="6.2">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
7 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
8 </package>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
9 <package name="R_3_0_1" version="3.0.1">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
10 <install version="1.0">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
11 <actions>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
12 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
13 <action type="set_environment_for_install">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
14 <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
15 <package name="atlas" version="3.10.1" />
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
16 </repository>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
17 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
18 <package name="readline" version="6.2" />
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
19 </repository>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
20 </action>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
21
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
22 <action language="cheetah" type="template_command">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
23 #set $cmd = './configure'
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
24 #if env.get('ATLAS_LIB_DIR', False):
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
25 #set $cmd += ' --with-blas="-L%s -lptf77blas -lpthread -latlas" ' % $env.ATLAS_LIB_DIR
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
26 #end if
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
27
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
28 #if env.get('READLINE_LIB_PATH', False):
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
29 export LDFLAGS=-L$env.READLINE_LIB_PATH &amp;&amp;
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
30 export CPPFLAGS=-I$env.READLINE_INCLUDE_PATH &amp;&amp;
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
31 #set $cmd += ' --with-readline=yes '
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
32 #else:
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
33 #set $cmd += ' --with-readline=no '
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
34 #end if
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
35
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
36 #set $cmd += ' --enable-R-shlib --with-x=no --libdir=%s/lib/ --bindir=%s/bin/ --datarootdir=%s/share/' % ($env.INSTALL_DIR, $env.INSTALL_DIR, $env.INSTALL_DIR)
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
37 $cmd
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
38 </action>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
39 <action type="shell_command">make</action>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
40 <action type="shell_command">make install</action>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
41 <action type="set_environment">
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
42 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
43 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
44 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
45 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
46 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
47 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
48 </action>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
49 </actions>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
50 </install>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
51 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
52 </package>
4aa16d4746cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
53 </tool_dependency>