Mercurial > repos > bgruening > precommit_test
changeset 14:b738c51af132 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 02 Nov 2013 20:43:44 -0400 |
| parents | 564b46e4fda7 |
| children | f7b208c7a3a1 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 17 insertions(+), 36 deletions(-) [+] |
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--- a/tool_dependencies.xml Sun Jun 30 19:30:17 2013 -0400 +++ b/tool_dependencies.xml Sat Nov 02 20:43:44 2013 -0400 @@ -1,52 +1,33 @@ <?xml version="1.0"?> <tool_dependency> - <package name="lapack" version="3.4.2"> - <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="atlas" version="3.10.1"> - <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <package name="perl" version="5.18.1"> + <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="readline" version="6.2"> - <repository changeset_revision="782fae4417eb" name="package_readline_6_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - - <package name="R_3_0_1" version="3.0.1"> + <package name="bioperl" version="1.6.922"> <install version="1.0"> <actions> - <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action> + <!-- install perl --> + <!--<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</action>--> + <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="atlas" version="3.10.1" /> - </repository> - <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="lapack" version="3.4.2" /> - </repository> - <repository changeset_revision="782fae4417eb" name="package_readline_6_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="readline" version="6.2" /> + <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> </repository> </action> - <!-- - with-blas="$LAPACK_LIB_DIR" - with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas" + <action type="shell_command">cpanm --local-lib=$INSTALL_DIR XML::Parser</action> + <action type="shell_command">cpanm --local-lib=$INSTALL_DIR Bundle::BioPerl</action> + - export BLAS=$LAPACK_LIB_DIR/libblas.a && - export LAPACK=$LAPACK_LIB_DIR/liblapack.a && - export ATLAS=$ATLAS_LIB_DIR/libatlas.a && -LD_LIBRARY_PATH - --> - <action type="shell_command"> - export LD_LIBRARY_PATH=$READLINE_LIB_PATH && - ./configure --with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas" --with-blas="$LAPACK_LIB_DIR" --enable-R-shlib --with-x=no --with-readline=yes --prefix=$INSTALL_DIR && make && make install - </action> <action type="set_environment"> - <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable> - <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> + <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR/lib</environment_variable> </action> </actions> </install> - <readme /> + <readme> + Bundle::BioPerl + </readme> </package> </tool_dependency>