Mercurial > repos > brenninc > test_r_cairo_oct1_2015
changeset 23:a2cce31a7295 draft
Deleted selected files
| author | brenninc |
|---|---|
| date | Fri, 02 Oct 2015 11:46:26 -0400 |
| parents | 070db1d479a6 |
| children | 1c8ae2960409 |
| files | packages.R r_info.sh r_info.xml tool_dependencies.xml |
| diffstat | 4 files changed, 0 insertions(+), 129 deletions(-) [+] |
line wrap: on
line diff
--- a/packages.R Fri Oct 02 06:46:47 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -library(Cairo) - -args<-commandArgs(TRUE) -writeLines(capture.output(sessionInfo()), args[1]) -sessionInfo()
--- a/r_info.sh Fri Oct 02 06:46:47 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/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"
--- a/r_info.xml Fri Oct 02 06:46:47 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -<tool id="brenninc_r_test" name="r_test" version="0.1.beta"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - <requirement type="package" version="0.0.3">R_cairo</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>
--- a/tool_dependencies.xml Fri Oct 02 06:46:47 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="atlas" version="3.10.2"> - <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="readline" version="6.3"> - <repository changeset_revision="40f8ebe365e9" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="cairo" version="1.14.2"> - <repository changeset_revision="9fe5875b0ede" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pixman" version="0.32.6"> - <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.5.2"> - <repository changeset_revision="55f81025bcb0" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="ncurses" version="6.0"> - <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="fontconfig" version="2.11.1"> - <repository changeset_revision="e1df54930f90" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.1.2"> - <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="4395fcf5d40c" prior_installation_required="True" /> - </package> - <package name="R_cairo" version="0.0.3"> - <install version="1.0"> - <actions> - <action type="setup_r_environment"> - <repository changeset_revision="40f8ebe365e9" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="readline" version="6.3" /> - </repository> - <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - <repository changeset_revision="9fe5875b0ede" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="cairo" version="1.14.2" /> - </repository> - <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pixman" version="0.32.6" /> - </repository> - <repository changeset_revision="55f81025bcb0" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.5.2" /> - </repository> - <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="ncurses" version="6.0" /> - </repository> - <repository changeset_revision="e1df54930f90" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="fontconfig" version="2.11.1" /> - </repository> - <repository changeset_revision="4395fcf5d40c" name="brenninc_r_sept32105" owner="brenninc" toolshed="https://testtoolshed.g2.bx.psu.edu/"> - <package name="R" version="3.1.2" /> - </repository> - <package>https://cran.r-project.org/src/contrib/Archive/Cairo/Cairo_1.5-8.tar.gz</package> - </action> - </actions> - </install> - </package> -</tool_dependency> - -