Mercurial > repos > shians > package_shrnaseq_1_2_1
view tool_dependencies.xml @ 6:1cf8c9ce7248
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author | shian_su <registertonysu@gmail.com> |
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date | Thu, 20 Nov 2014 15:05:03 +1100 |
parents | b09185fed619 |
children | e35291a2d6fa |
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<?xml version="1.0"?> <tool_dependency> <package name="R_3_1_1" version="3.1.1"> <repository name="package_r_3_1_1" owner="fubar" prior_installation_required="True" /> </package> <package name="shrnaseq" version="1.2.1"> <install version="1.0"> <actions> <action type="set_environment_for_install"> <repository name="package_r_3_1_1" owner="fubar" /> <package name="R_3_1_1" version="3.1.1" /> </repository> </action> <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/locfit_1.5-9.1.tar.gz</action> <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/statmod_1.4.20.tar.gz</action> <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/limma_3.22.1.tar.gz</action> <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/edgeR_3.8.3.tar.gz</action> <action type="make_directory">$INSTALL_DIR/shrnaseq/</action> <action type="shell_command"> export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR/deseq2/ && Rscript -e "install.packages(c('locfit_1.5-9.1.tar.gz', 'statmod_1.4.20.tar.gz', 'limma_3.22.1.tar.gz', 'edgeR_3.8.3.tar.gz'),lib='$INSTALL_DIR/shrnaseq/', repos=NULL, dependencies=FALSE)" </action> <action type="set_environment"> <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/shrnaseq/</environment_variable> </action> </actions> </install> <readme> shrnaseq analysis using edgeR bioConductor package. http://bioconductor.org/packages/release/bioc/html/edgeR.html </readme> </package> </tool_dependency>