Mercurial > repos > bgruening > package_deseq2_1_0_17
changeset 6:ec26508b1a2a draft
Uploaded
author | bgruening |
---|---|
date | Mon, 30 Sep 2013 12:51:19 -0400 |
parents | 3e3d1a50a347 |
children | b7272a300fce |
files | tool_dependencies.xml |
diffstat | 1 files changed, 31 insertions(+), 26 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Sep 16 10:09:20 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 30 12:51:19 2013 -0400 @@ -1,48 +1,53 @@ <?xml version="1.0"?> <tool_dependency> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="bae5c9880b71" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" 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="setup_r_environment"> - - <repository name="package_r_3_0_1" owner="bgruening"> + <action type="set_environment_for_install"> + <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="R_3_0_1" version="3.0.1" /> </repository> - - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/IRanges_1.18.2.tar.gz</r_package> - - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/GenomicRanges_1.12.4.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Rcpp_0.10.4.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RcppArmadillo_0.3.900.0.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Biobase_2.20.1.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DBI_0.2-7.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RSQLite_0.11.4.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/AnnotationDbi_1.22.6.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/xtable_1.7-1.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/XML_3.98-1.1.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/annotate_1.38.0.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/genefilter_1.42.0.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RColorBrewer_1.0-5.tar.gz</r_package> - <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DESeq2_1.0.18.tar.gz</r_package> - </action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/IRanges_1.18.2.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/GenomicRanges_1.12.4.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Rcpp_0.10.4.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RcppArmadillo_0.3.900.0.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Biobase_2.20.1.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DBI_0.2-7.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RSQLite_0.11.4.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/AnnotationDbi_1.22.6.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/xtable_1.7-1.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/XML_3.98-1.1.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/annotate_1.38.0.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/genefilter_1.42.0.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RColorBrewer_1.0-5.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DESeq2_1.0.18.tar.gz</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/rjson_0.2.13.tar.gz</action> + <!--<action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/biomaRt_2.16.0.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 "install.packages(c('BiocGenerics_0.6.0.tar.gz','IRanges_1.18.2.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','Biobase_2.20.1.tar.gz','DBI_0.2-7.tar.gz','RSQLite_0.11.4.tar.gz','AnnotationDbi_1.22.6.tar.gz','xtable_1.7-1.tar.gz','XML_3.98-1.1.tar.gz','annotate_1.38.0.tar.gz','genefilter_1.42.0.tar.gz','RColorBrewer_1.0-5.tar.gz','DESeq2_1.0.18.tar.gz', 'rjson_0.2.13.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</environment_variable> + <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable> </action> - </actions> </install> <readme> Differential gene expression analysis based on the negative binomial distribution. http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html + Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so </readme> </package> </tool_dependency>