Mercurial > repos > brenninc > test_r_cairo_oct1_2015
changeset 0:d03274c7c546 draft
Uploaded
| author | brenninc |
|---|---|
| date | Thu, 01 Oct 2015 05:23:19 -0400 |
| parents | |
| children | 110f8e93a946 |
| files | packages.R r_info.sh r_info.xml tool_dependencies.xml |
| diffstat | 4 files changed, 156 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/packages.R Thu Oct 01 05:23:19 2015 -0400 @@ -0,0 +1,22 @@ +library(acepack) +library(colorspace) +library(dichromat) +library(digest) +library(Formula) +library(gtable) +library(labeling) +library(magrittr) +library(proto) +library(Rcpp) +library(RColorBrewer) +library(rjson) +library(snow) +library(SparseM) +library(stringi) +library(stringr) +library(XML) +library(xtable) + +args<-commandArgs(TRUE) +writeLines(capture.output(sessionInfo()), args[1]) +sessionInfo()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_info.sh Thu Oct 01 05:23:19 2015 -0400 @@ -0,0 +1,30 @@ +#!/bin/sh + + +#Copied from https://github.com/galaxyproject/galaxy/blob/dev/tools/stats/r_wrapper.sh + +### Run R providing the R script in $1 as standard input and passing +### the remaining arguments on the command line + +# Function that writes a message to stderr and exits +fail() +{ + echo "$@" >&2 + exit 1 +} + +# Ensure R executable is found +which R > /dev/null || fail "'R' is required by this tool but was not found on path" + +# Extract first argument +rfile=$1 +package_file=$2 +version_file=$3 + +# Ensure the file exists +test -f $infile || fail "R input file '$infile' does not exist" + +# Invoke R passing file named by first argument to stdin +#Remove --slave for full R output +R --vanilla --slave --args $package_file < $rfile +echo "done"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_info.xml Thu Oct 01 05:23:19 2015 -0400 @@ -0,0 +1,30 @@ +<tool id="r_extended_level_one_sessioninfo" name="r_extended_level_one sessionInfo" version="0.1.beta"> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="0.0.1">R_mulitple</requirement> + <!--requirement type="package" version="2.0-0">R_dichroma</requirement--> + </requirements> + <description>Lists packages installed into R</description> + <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> +<![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> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Oct 01 05:23:19 2015 -0400 @@ -0,0 +1,74 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository toolshed="http://l-unxx4770.it.manchester.ac.uk:9009/" name="package_r_3_1_2" owner="brenninc" changeset_revision="6c7b9b5dfcae" prior_installation_required="True" /> + </package> + <package name="R_extend_level_one" version="0.0.1"> + <install version="1.0"> + <actions> + <action type="setup_r_environment"> + <repository changeset_revision="6c7b9b5dfcae" name="package_r_3_1_2" owner="brenninc" toolshed="http://l-unxx4770.it.manchester.ac.uk:9009/"> + <package name="R" version="3.1.2" /> + <!-- includes base, boot, + class, cluster, codetools, compiler, + datasets, + foreign, + graphics, grDevices, grid, + KernSmooth, + lattice, + MASS, Matrix, methods, mgcv, + nlme, nnet, + parallel, + rpart, + spatial, splines, stats, stats4, survival, + tcltk, tools, + utils--> + + </repository> + <!--No dependencies Not on https://bioarchive.galaxyproject.org --> + <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package> + <!-- Imports graphics + Suggests: KernSmooth, MASS, kernlab, mvtnorm, vcd, dichromat, tcltk--> + <package>https://cran.r-project.org/src/contrib/digest_0.6.8.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package> + <!-- Depends stats --> + <package>https://cran.r-project.org/src/contrib/Formula_1.2-1.tar.gz</package> + <!-- Depends stats --> + <package>https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz</package> + <!-- Depends grid + Suggests: testthat, plyr--> + <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package> + <!-- Suggests: testthat, knitr --> + <package>https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz</package> + <!-- Suggests: graph, Rgraphviz --> + <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.0.tar.gz</package> + <!-- Imports: methods, utils + Suggests: RUnit, inline, rbenchmark, highlight, pkgKitten (≥ 0.1.2) --> + <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/snow_0.3-13.tar.gz</package> + <!-- Depends: R (≥ 2.12.1), utils + Suggests: Rmpi, rpvm, rlecuyer, rsprng, nws --> + <package>https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz</package> + <!-- Depends: R (≥ 2.15), methods + Imports: graphics, stats, utils --> + <package>https://cran.r-project.org/src/contrib/stringi_0.5-5.tar.gz</package> + <!-- Depends: R (≥ 2.13.1) + Imports: tools, utils, stats --> + <package>https://cran.r-project.org/src/contrib/XML_3.98-1.3.tar.gz</package> + <!-- Depends: R (≥ 2.13.0), methods, utils + Suggests: bitops, RCurl --> + <package>https://cran.r-project.org/src/contrib/xtable_1.7-4.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz</package> + <!-- Depends: R (≥ 2.14) + Imports: stringi (≥ 0.4.1), magrittr + Suggests: testthat, knitr --> + </action> + </actions> + </install> + </package> +</tool_dependency> + +