Mercurial > repos > bgruening > precommit_test
changeset 11:4e9dce1105cd draft
Uploaded
author | bgruening |
---|---|
date | Sun, 30 Jun 2013 15:34:58 -0400 |
parents | 5b253fafd35a |
children | 856591655486 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 49 insertions(+), 2 deletions(-) [+] |
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--- a/tool_dependencies.xml Thu Jun 06 02:44:50 2013 -0400 +++ b/tool_dependencies.xml Sun Jun 30 15:34:58 2013 -0400 @@ -1,6 +1,53 @@ <?xml version="1.0"?> <tool_dependency> - <package name="fastqc_dist_0_10_1" version="0.10.1"> - <repository changeset_revision="7d57dba74532" name="upload_testing" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <!-- + <package name="lapack" version="3.4.2"> + <repository name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" /> + </package> + <package name="atlas" version="3.10.1"> + <repository name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" /> + </package> + + <package name="readline" version="6.2"> + <repository name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + --> + + <package name="R_3_0_1" version="3.0.1"> + <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> + + <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> + </action> + <!-- + with-blas="$LAPACK_LIB_DIR" + with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas" + + export BLAS=$LAPACK_LIB_DIR/libblas.a && + export LAPACK=$LAPACK_LIB_DIR/liblapack.a && + export ATLAS=$ATLAS_LIB_DIR/libatlas.a && + --> + + <action type="set_environment_for_install"> + <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="readline" version="6.2" /> + </repository> + </action> + <action type="shell_command">./configure --enable-R-shlib --with-x=no --with-readline=no --prefix=$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> + </action> + </actions> + </install> + <readme /> </package> </tool_dependency>