* 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)
* fix bioconductor package install docs for multi-task race condition
* fix typos
* remove docs on updating an existing cluster's packages from within the foreach loop
* support an install_bioconductor.R script
* update docs with working sample
* initial command line instructions for bioconductor
* initial startup scripts for installing bioconductor
* fix if then syntax
* force update node environment with update path for R runtime
* install bioconductor
* wrap bioconductor install command in Rscript
* bioconductor sample docs
* update bioC docs
* remove .gitignore rule for .json files
* add pointer to BioC cluster config from docs
* update docs to include github auth feature
* pr feedback for more verbose context
* move github auth instructions to pacakge management document
* remove github specific link from readme
* put images into vignette folder
* Created 00-azure-introduction.md
* Created 10-vm-sizes.md
* Update VM sizes link in docs/README.md
* Create 20-package-management.md
* Updated README.md with Azure Batch limitations
* Create 21-distributing-data.md
* Create 22-parallelizing-cores.md
* Create 23-persistent-storage.md
* standardized foreach keyword and pool keyword
Brian
zfengms
Pablo Selem
JS