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doAzureParallel
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doAzureParallel/samples/azure_files/azure_files_cluster.json

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Feature/add azure files cluster config (#108) * 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 * add missing azureFiles cluster config to samples
2017-09-07 23:49:28 +03:00
{
"name": "azurefiles",
"vmSize": "Standard_D2_v2",
"maxTasksPerNode": 1,
"poolSize": {
"dedicatedNodes": {
"min": 0,
"max": 0
},
"lowPriorityNodes": {
"min": 2,
"max": 2
},
"autoscaleFormula": "QUEUE"
},
"rPackages": {
"cran": [],
"github": [],
Feature/configfromobj support programmatically created credentials and cluster configs (#168) * support programmatically generated credentials/cluster config * update docs for programmatically generated config * reformat code * styling fixes * combine credentials cluster config methods * fix set credentials issue and test input * do not create az_config.json * update messages * move githubAuthenticationToken from cluster config to credentials
2017-11-17 10:18:09 +03:00
"bioconductor": []
Feature/add azure files cluster config (#108) * 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 * add missing azureFiles cluster config to samples
2017-09-07 23:49:28 +03:00
},
"commandLine": [
Feature/container (#153) * 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)
2017-11-03 20:06:40 +03:00
"mkdir /mnt/batch/tasks/shared/data",
Fix: File share sample (#312) * Fixed sample * Removed unchanged file name * removed account * Removed custom script
2018-09-19 00:44:00 +03:00
"mount -t cifs //<STORAGE_ACCOUNT_NAME>.file.core.windows.net/<FILE_SHARED_NAME> /mnt/batch/tasks/shared/data -o vers=3.0,username=<STORAGE_ACCOUNT_NAME>,password=<STORAGE_ACCOUNT_KEY>,dir_mode=0777,file_mode=0777,sec=ntlmssp"
Feature/custom package (#272) * Added custom package script * Added feature custom download * Fixed typo * Fixed directory for installation * Fixed full folder directory * Add dependencies and fix pattern * Fix pattern not found * Added repo * Switching to devtools * Fixing devtools install with directory * Fix in for merger.R * Working cluster custom packages * Removed printed statements * Working on custom docs * Custom packages sample docs * Fixed typo in azure files typo * Fixed typos based on PR
2018-05-14 23:47:00 +03:00
]
Feature/container (#153) * 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)
2017-11-03 20:06:40 +03:00
}