* 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)
* Added set chunk size
* Adding resource files on pool creation
* renaming generate file functions
* Moved worker/merger scripts to doAzureParallel and created common job env
* Added stdout and stderr logs in uploads
* added to docs / README
* Switched params for cluster and added examples
* setCreds, resizeCluster, job management
* cred generator update
* Added samples, moved autoscale, and low-pri/output files
* Added documentation on methods for ??R feature
* Added export for makeCluster
* Namespace missing export
* clusterSetting param name
* cluster id param name
* NumOfNodes param for wait nodes completion fix
* Added proper naming for registerDoAzureParallel
* readme update'
* typo readme
* low pri in readme
* monte carlo simulation
* Added new sample for sas resource files
* caret + annotation on montecarlo sim
* samples readme.md
* samples readme
* Fixed the resource files to use proper storage account for example
* Update README.md
* Update 11-autoscale.md
* Fixed autoscale formula for task queue to take maxTaskPerNode
* Added named args to createSasToken
* Update resource-files-example.R
* Update 21-distributing-data.md
* Renamed samples files to underscore format
* Update 21-distributing-data.md
* Update README.md
* Update README.md
* Update README.md
* Edited changelog file
* Update plyr_example.R
* Update README.md
Pablo Selem
JS
Brian