Mercurial > repos > bgruening > package_deseq2_1_0_17
changeset 3:6d4dbaa47b83 draft
Uploaded
author | bgruening |
---|---|
date | Fri, 02 Aug 2013 07:33:28 -0400 |
parents | adb7a2fbdbbb |
children | eab36a9a70b1 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 18 insertions(+), 3 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Jul 01 08:23:50 2013 -0400 +++ b/tool_dependencies.xml Fri Aug 02 07:33:28 2013 -0400 @@ -1,23 +1,38 @@ <?xml version="1.0"?> <tool_dependency> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="1d5580f2ece0" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4dba1ce455da" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.0.17"> <install version="1.0"> <actions> <action type="set_environment_for_install"> - <repository changeset_revision="1d5580f2ece0" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="4dba1ce455da" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="R_3_0_1" version="3.0.1" /> </repository> </action> +<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz</action> +<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/IRanges_1.18.2.tar.gz</action> +<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/annotate_1.38.0.tar.gz</action> +<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/GenomicRanges_1.12.4.tar.gz</action> +<action type="download_file">http://cran.fhcrc.org/src/contrib/Rcpp_0.10.4.tar.gz</action> +<action type="download_file">http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.3.900.0.tar.gz</action> +<action type="download_file">http://cran.fhcrc.org/src/contrib/locfit_1.5-9.1.tar.gz</action> +<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/genefilter_1.42.0.tar.gz</action> +<action type="download_file">http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz</action> +<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/DESeq2_1.0.18.tar.gz</action> + + + <action type="make_directory">$INSTALL_DIR/deseq2/</action> <action type="shell_command"> export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR/deseq2/ && - Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite('DESeq2')" + + Rscript -e "install.packages(c("BiocGenerics_0.6.0.tar.gz","IRanges_1.18.2.tar.gz","annotate_1.38.0.tar.gz","GenomicRanges_1.12.4.tar.gz","Rcpp_0.10.4.tar.gz","RcppArmadillo_0.3.900.0.tar.gz","locfit_1.5-9.1.tar.gz","genefilter_1.42.0.tar.gz","RColorBrewer_1.0-5.tar.gz","DESeq2_1.0.18.tar.gz",),lib="$INSTALL_DIR/deseq2/", repos=NULL, dependencies=FALSE)" + </action> <action type="set_environment"> <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>