Mercurial > repos > brenninc > brenninc_test
changeset 4:9d4fe3e641c0 draft
Uploaded
| author | brenninc |
|---|---|
| date | Wed, 13 Apr 2016 11:48:32 -0400 |
| parents | 601f53aa6973 |
| children | 951b3ab4c314 |
| files | packages.R r_info.xml tool_dependencies.xml |
| diffstat | 3 files changed, 31 insertions(+), 228 deletions(-) [+] |
line wrap: on
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--- a/packages.R Tue Apr 12 04:23:41 2016 -0400 +++ b/packages.R Wed Apr 13 11:48:32 2016 -0400 @@ -1,101 +1,7 @@ -library(BiocGenerics) -library(S4Vectors) -library(IRanges) -library(GenomeInfoDb) -library(XVector) -library(GenomicRanges) -library(Rcpp) -library(RcppArmadillo) -library(Biobase) -library(lambda.r) -library(futile.options) -library(futile.logger) -library(snow) -library(BiocParallel) -library(DBI) -library(RSQLite) -library(AnnotationDbi) -library(XML) -library(xtable) -library(annotate) -library(survival) -library(genefilter) -library(lattice) -library(locfit) -library(RColorBrewer) -library(geneplotter) -library(plyr) -library(digest) -library(gtable) -library(stringi) -library(magrittr) -library(stringr) -library(reshape2) -library(dichromat) -library(colorspace) -library(munsell) -library(labeling) -library(scales) -library(proto) -library(MASS) -library(ggplot2) -library(Formula) -library(latticeExtra) -library(cluster) -library(rpart) -library(nnet) -library(acepack) -library(foreign) -library(gridExtra) -library(Hmisc) -library(DESeq2) -library(modeltools) -library(flexmix) -library(brew) -library(Rook) -library(rjson) -library(Cairo) -library(limma) -library(edgeR) -library(RMTstat) -library(Lmoments) -library(distillery) -library(nlme) -library(Matrix) -library(mgcv) -library(minqa) -library(nloptr) -library(RcppEigen) -library(lme4) -library(pbkrtest) -library(SparseM) -library(MatrixModels) -library(quantreg) -library(car) -library(extRemes) -library(pcaMethods) -library(scde) -library(evaluate) -library(formatR) -library(highr) -library(mime) -library(markdown) -library(yaml) -library(knitr) -library(proxy) -library(cba) -library(fastcluster) -library(dynamicTreeCut) -library(matrixStats) -library(impute) -library(codetools) -library(iterators) -library(foreach) -library(doParallel) -library(reshape) -library(preprocessCore) -library(GO.db) -library(WGCNA) +installed_packages_info = installed.packages() +installed_packages = installed_packages_info[,1] + +lapply(installed_packages, require, character.only = TRUE) args<-commandArgs(TRUE) writeLines(capture.output(sessionInfo()), args[1])
--- a/r_info.xml Tue Apr 12 04:23:41 2016 -0400 +++ b/r_info.xml Wed Apr 13 11:48:32 2016 -0400 @@ -1,29 +1,34 @@ <tool id="r_exended_lister" name="r extended lister" version="0.1.beta"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - <!--requirement type="package" version="0.0.1">R_extended</requirement--> - </requirements> - <description>Lists packages installed into R</description> - <stdio> + <description>Lists packages installed into R</description> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <!--requirement type="package" version="0.0.1">R_extended</requirement--> + </requirements> + <stdio> <exit_code range="1" level="fatal" description="Error code 1 occurred" /> <exit_code range="2:255" level="fatal" description="Unknown error occurred" /> - </stdio> - <command interpreter="bash"> - r_info.sh $__tool_directory__/packages.R $packages - </command> - <outputs> - <data format="txt" name="packages" label="R Session Info"/> - </outputs> - - <tests> - </tests> - - <help> + </stdio> + <command interpreter="bash"> + r_info.sh $__tool_directory__/packages.R $packages + </command> + <outputs> + <data format="txt" name="packages" label="R Session Info"/> + </outputs> + <tests> + <test> + <output name="out_file1"> + <assert_contents> + <has_text text="Matrix_1.2-1" /> + </assert_contents> + </output> + </test> + </tests> + <help> <![CDATA[ This is a verification tool to see exactly which R this galaxy server is using. It will outout the R version info and the R packages installed. ]]> - </help> - + </help> + <citations/> </tool>
--- a/tool_dependencies.xml Tue Apr 12 04:23:41 2016 -0400 +++ b/tool_dependencies.xml Wed Apr 13 11:48:32 2016 -0400 @@ -1,115 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.2.1"> - <repository changeset_revision="3f2e129aae27" name="brenninc_r_oct9_2015" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1eda5afe26d0" name="package_r_3_2_1" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <!--package name="R_extended" version="0.0.1"> - <install version="1.0"> - <actions> - <action type="setup_r_environment"> - <repository name="package_r_3_2_1" owner="brenninc" prior_installation_required="True" > - <package name="R" version="3.2.1" /> - </repository> - <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/BiocGenerics_0.14.0.tar.gz</package> - <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/S4Vectors_0.6.6.tar.gz</package> - 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