a6e51c964e
* force add PATH to current user * checkin docker setup script * Update cluster_setup.sh * install docker and start container on cluster setup * WIP: Run task in container * fix merge conflict * run tasks and merge task from within container * refactor code to proper docker commands and make a single R container per job * refactor command line utils into its own file * refactor job utilities into its own file * move cluster setup script to inst folder * remove unnecessary curl installs * remove starting container from setup script * check in WIP * add apt_install file * make required directories * update cluster setup files as needed * include libxml2 packages in apt installs * working cluster create with cran and github dependencies * update job prep to install apt-get and not each task * use rocker containers instead of r-base * remove unused & commented code * remove unused install function * address several lintr issues * initial test dockerfile * add spacing between commands * temporarily point wget to feature branch * update bioconductor install for non-jobPrep installs * Delete Dockerfile * minor changes to install bioc * resolve merge conflicts * update cluster to correctly install BioC packages using install_bioconductor * fix issue where some packages were not getting installed * add missing BioConductorCommand initializer * remove print lines * initial dockerfile implementations * update docker files * Only install packages if they are required * Remove requirement on bioconductor installer script on start task * remove duplicate environment variable entry * update docs for container support * update version to 0.6.0 * refactor changes updates * remove poorly formatted whitespaces * add full path to pacakges directory * fix docker command line * update file share sample * update azure files cluster name * update mandelbrot sample * update package management sample * update plyr samples * make montecarlo sample more consistent * update montecarlo sample * remove plyr example * fix bad environment pointer * fix linter issues * more linter fixes * more linter issues * use latest rAzureBatch version * update resource files example * remove reference to deleted sample * pr feedback * PR docs feedback * Print errors from worker (#154) * Fixed pool package command line lintr test * Package installation tests fixed - too long lines * Fixed json in customize cluster docs * Fix: Typos in customize cluster docs * Cleaning up files * Feature/githubbiopackage (#150) * install github package worked for foreach loop * fix lintr error * tests for github and bioc packages installation * lintr fix * add back lost code due to merge and update docs * The Travis CI build failed for feature/githubbiopackage * remove incorrect parameter for install_github * Updated job prep task to have default command * Use the latest version of rAzureBatch * Updated description + Generate cluster config * Fix: Bioconductor and Github packages installation (#155) * Added multiple package install test and fix obj reading args * Fixed naming for packages install * Replaced validation exclusion for linter * Fixed test validate test * Fixing all interactive tests with skip * Fixed renaming validation * Removed default test - cannot be tested * Removed in validation * Added cluster package install tests (#156) |
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