Mercurial > repos > morinlab > package_expands_1_7_2
changeset 1:b5ab09203060 draft default tip
Uploaded
| author | morinlab |
|---|---|
| date | Sun, 04 Dec 2016 17:31:48 -0500 |
| parents | 47e78ffd147e |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 73 insertions(+), 94 deletions(-) [+] |
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--- a/tool_dependencies.xml Sun Dec 04 17:30:17 2016 -0500 +++ b/tool_dependencies.xml Sun Dec 04 17:31:48 2016 -0500 @@ -1,97 +1,76 @@ <?xml version="1.0"?> <tool_dependency> - <package name="R" version="3.1.2"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action sha256sum="586dde39d6821bcc5079004450f5d19f836a26d4554083c7add3933f071451e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.1.2_linux_x64.tar.gz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <action type="set_environment"> - <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> - <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> - </action> - </actions> - <actions> - <action sha256sum="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a" type="download_by_url">https://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action> - <package name="readline" version="6.2"> - <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="cairo" version="1.12.14"> - <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pixman" version="0.32.4"> - <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.5.2"> - <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="ncurses" version="5.9"> - <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="fontconfig" version="2.11.1"> - <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <action type="set_environment_for_install"> - <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="readline" version="6.2" /> - </repository> - <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="cairo" version="1.12.14" /> - </repository> - <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pixman" version="0.32.4" /> - </repository> - <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.5.2" /> - </repository> - <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="ncurses" version="5.9" /> - </repository> - <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="fontconfig" version="2.11.1" /> - </repository> - </action> - <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action> - <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> - <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> - </actions> - <action type="set_environment"> - <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> - <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable> - <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable> - <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable> - <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> - <!-- Include library with local rJava installation --> - <environment_variable action="prepend_to" name="R_LIBS">/usr/lib/R/site-library</environment_variable> - <!-- Set JAVA_HOME & LD_LIBRARY_PATH --> - <environment_variable action="set_to" name="JAVA_HOME">/usr/lib/jvm/java-8-openjdk-amd64/jre</environment_variable> - <environment_variable action="set_to" name="LD_LIBRARY_PATH">/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server</environment_variable> - <!-- Set FONTCONFIG_PATH for R png output --> - <environment_variable action="set_to" name="FONTCONFIG_PATH">$INSTALL_DIR/etc/fonts</environment_variable> - <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> - <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <!-- Append java bin to PATH --> - <environment_variable action="append_to" name="PATH">$JAVA_HOME/bin</environment_variable> - </action> - </actions_group> - </install> - <readme> - The precompiled versions of this package were built 2014-12-21. - R is a free software environment for statistical computing and graphics. - NOTE: See custom compilation options above. - </readme> - </package> + + <!-- R --> + <package name="R" version="3.1.2"> + <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <!-- Morinlab scripts with EXPANDS wrapper script --> + <package name="morinlab_scripts" version="14.2"> + <repository changeset_revision="b88b230de028" name="package_morinlab_scripts_14_2" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <!-- EXPANDS and other R packages --> + <package name="expands" version="1.7.2"> + + <install version="1.0"> + <actions> + + <action type="set_environment_for_install"> + <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="R" version="3.1.2" /> + </repository> + </action> + + <action type="shell_command">R CMD javareconf -e</action> + + <action type="setup_r_environment"> + <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="R" version="3.1.2" /> + </repository> + <package>https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/mclust_5.2.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/nnet/nnet_7.3-11.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/flexmix_2.3-13.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/nlme/nlme_3.1-122.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/ape_3.5.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/permute_0.9-0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/moments_0.14.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/argparser_0.4.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/matlab_1.0.2.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/digest/digest_0.6.9.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.12.5.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.3.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/stringi/stringi_1.0-1.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/stringr/stringr_0.6.2.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/reshape2/reshape2_1.4.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/munsell/munsell_0.4.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.3.0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/ggrepel_0.5.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/DBI/DBI_0.4-1.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/R6/R6_2.1.1.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Archive/BH/BH_1.60.0-1.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/expands_1.7.2.tar.gz</package> + </action> + </actions> + + </install> + + </package> + <readme> + Expanding Ploidy and Allele Frequency on Nested Subpopulations (EXPANDS) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome-sequencing input data. + </readme> </tool_dependency>