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comparison tool_dependencies.xml @ 14:b738c51af132 draft

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author bgruening
date Sat, 02 Nov 2013 20:43:44 -0400
parents 564b46e4fda7
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13:564b46e4fda7 14:b738c51af132
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="lapack" version="3.4.2"> 3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="atlas" version="3.10.1"> 6 <package name="bioperl" version="1.6.922">
7 <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="readline" version="6.2">
10 <repository changeset_revision="782fae4417eb" name="package_readline_6_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package>
12
13 <package name="R_3_0_1" version="3.0.1">
14 <install version="1.0"> 7 <install version="1.0">
15 <actions> 8 <actions>
16 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action> 9 <!-- install perl -->
10 <!--<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</action>-->
11 <!-- populate the environment variables from the dependend repos -->
17 <action type="set_environment_for_install"> 12 <action type="set_environment_for_install">
18 <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> 13 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
19 <package name="atlas" version="3.10.1" /> 14 <package name="perl" version="5.18.1" />
20 </repository>
21 <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
22 <package name="lapack" version="3.4.2" />
23 </repository>
24 <repository changeset_revision="782fae4417eb" name="package_readline_6_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
25 <package name="readline" version="6.2" />
26 </repository> 15 </repository>
27 </action> 16 </action>
28 17
29 <!-- 18 <action type="shell_command">cpanm --local-lib=$INSTALL_DIR XML::Parser</action>
30 with-blas="$LAPACK_LIB_DIR" 19 <action type="shell_command">cpanm --local-lib=$INSTALL_DIR Bundle::BioPerl</action>
31 with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas"
32 20
33 export BLAS=$LAPACK_LIB_DIR/libblas.a &amp;&amp; 21
34 export LAPACK=$LAPACK_LIB_DIR/liblapack.a &amp;&amp;
35 export ATLAS=$ATLAS_LIB_DIR/libatlas.a &amp;&amp;
36 LD_LIBRARY_PATH
37 -->
38 <action type="shell_command">
39 export LD_LIBRARY_PATH=$READLINE_LIB_PATH &amp;&amp;
40 ./configure --with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas" --with-blas="$LAPACK_LIB_DIR" --enable-R-shlib --with-x=no --with-readline=yes --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install
41 </action>
42 <action type="set_environment"> 22 <action type="set_environment">
43 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> 23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
44 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> 24 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
45 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable> 25 <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR/lib</environment_variable>
46 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
47 </action> 26 </action>
48 </actions> 27 </actions>
49 </install> 28 </install>
50 <readme /> 29 <readme>
30 Bundle::BioPerl
31 </readme>
51 </package> 32 </package>
52 </tool_dependency> 33 </tool_dependency>