Merge branch 'master' into 3036-collection-uuids
[arvados.git] / crunch_scripts /
2014-08-19 Peter AmstutzMerge branch 'master' into 3036-collection-uuids
2014-08-18 Tom Clegg3114: Merge branch 'master' into 3114-copy-to-project
2014-08-16 Tom CleggMerge branch '2800-python-global-state' into 2800-pgs
2014-08-14 Tom Clegg3551: Merge branch 'master' into 3551-go-layout
2014-08-14 Peter AmstutzMerge branch '3505-virtual-work-dir' refs #3505
2014-08-14 Peter AmstutzMerge branch 'master' into 3505-virtual-work-dir
2014-08-14 Peter Amstutz3505: tinker with logging
2014-08-14 Peter Amstutz3505: Fix typo in run-command
2014-08-14 Peter Amstutz3505: Move helper scripts into crunchutil module. ...
2014-08-13 Tom Clegg3551: Merge branch 'master' into 3551-go-layout
2014-08-13 Peter Amstutz3505: Fixed typo comparison of list against 0 instead...
2014-08-13 Peter Amstutz3505: Adjust order of initialization to reflect potenti...
2014-08-13 Peter AmstutzAdded virtual working directory "task.vwd" option to...
2014-08-12 radhikaMerge branch 'master' into 3296-user-profile
2014-08-12 Tom CleggMerge branch '3531-sort-jobs-with-pipelines' closes...
2014-08-12 Peter AmstutzFix regular expression in decompress-all.py refs ...
2014-08-12 Peter AmstutzFix syntax error in decompress-all.py refs #3373
2014-08-12 Peter AmstutzMerge branch '3373-improve-gatk3-snv-pipeline' closes...
2014-08-12 Peter Amstutz3373: Test filename extension before attempting to...
2014-08-08 Peter Amstutz3373: split-fastq: Fix loop
2014-08-08 Peter Amstutz3373: split-fastq: Fix regex again
2014-08-08 Peter Amstutz3373: Fix wrong regex group
2014-08-08 Peter Amstutz3373: Fix syntax error in split-fastq
2014-08-08 Peter Amstutz3373: more run-command cleanup, global p -> taskp,...
2014-08-08 Peter Amstutz3373: Switch run-command to use python logging instead...
2014-08-08 Peter Amstutz3373: split-fastq: merge loops to capture both single...
2014-08-08 Peter Amstutz3373: decompress-all: cleaned up code a bit. Fail...
2014-08-07 Peter AmstutzMerge branch 'master' into 3373-improve-gatk3-snv-pipeline
2014-08-06 Peter AmstutzMerge branch 'master' into 3373-improve-gatk3-snv-pipeline
2014-08-05 Peter AmstutzDisable chunking
2014-08-05 Peter AmstutzChunking fastq seems to work, but is very slow.
2014-08-05 Peter Amstutzarvados.LOCATOR
2014-08-05 Peter Amstutzimport string
2014-08-05 Peter AmstutzFix syntax error
2014-08-05 Peter AmstutzCheck for None
2014-08-05 Peter AmstutzWorking on split-fastq to actually split the fastq...
2014-08-05 Peter AmstutzRenamed "job.src" to "job.srcdir", "job.id" to "job...
2014-08-04 Peter Amstutz$(link ...) now expects complete path.
2014-08-04 Peter AmstutzMerge branch 'master' into 3373-improve-gatk3-snv-pipeline
2014-08-04 Peter AmstutzMerge branch '3373-improve-gatk3-snv-pipeline' of git...
2014-08-04 Peter AmstutzSimplified collection-merge. Added comments to collect...
2014-08-04 Peter AmstutzWorks now
2014-08-04 Peter Amstutzfix parameters
2014-08-04 Peter AmstutzDecompress-all wip
2014-08-01 Peter AmstutzAdded $(task.outdir) and $(job.src)
2014-07-30 Peter AmstutzFix $(node.cores)
2014-07-30 Peter Amstutzstr or unicode
2014-07-30 Peter Amstutzextra / after dir
2014-07-30 Peter AmstutzBetter error from glob
2014-07-30 Peter AmstutzPretty print
2014-07-30 Peter AmstutzRearranged exception handling a little more
2014-07-30 Peter AmstutzMore logging
2014-07-30 Peter AmstutzPrint traceback on exception
2014-07-30 Peter AmstutzSet first task to success
2014-07-30 Peter Amstutzimport copy
2014-07-30 Peter Amstutz.st_mode
2014-07-30 Peter Amstutzimport stat
2014-07-30 Peter AmstutzFix syntax error
2014-07-30 Peter AmstutzRefactored and generalized list expansion, can use...
2014-07-30 Peter AmstutzSimpler split-fastq, doesn't try to upload the collecti...
2014-07-29 Peter AmstutzChange collection create request
2014-07-29 Peter AmstutzDebug manifest format to see why api server is rejecting it
2014-07-29 Peter Amstutzdebug print manifest_text
2014-07-29 Peter AmstutzLeft debugging in by accident
2014-07-29 Peter AmstutzSame bug, different place
2014-07-29 Peter AmstutzInput is "reads" not "input"
2014-07-29 Peter Amstutztypo fix get_job_param() -> getjobparam()
2014-07-29 Peter Amstutzforeach just refers to other parameter to use as iterat...
2014-07-29 Peter AmstutzAdded "foreach" to run-command wrapper. Needs testing.
2014-07-29 Peter AmstutzDon't split fastq, just organize into directories.
2014-07-29 Peter AmstutzFull split-fastq wip
2014-07-09 radhikaMerge branch 'master' into 3106-modal-loading-indicator
2014-07-08 Peter AmstutzMerge branch 'resumable-output-upload'. Adds signal...
2014-07-08 Peter AmstutzActually use the resume cache
2014-07-08 radhikaMerge branch 'master' into 3203-workbench-tutorial
2014-07-08 Peter AmstutzTurns out sys.exit runs finally: blocks.
2014-07-08 Peter AmstutzAdd debugging
2014-07-08 Peter AmstutzWrong num args
2014-07-08 Peter AmstutzSigHandler object
2014-07-08 Peter AmstutzStill messing with signals.
2014-07-08 Peter AmstutzFix wrong number of parameters
2014-07-08 Peter AmstutzRecord signals a different way
2014-07-08 Peter AmstutzMore work on signal handling
2014-07-08 Peter AmstutzForward signals to process.
2014-07-08 Peter AmstutzUse resumable upload writing output in run-command
2014-07-08 radhikaMerge branch 'master' into 2380-ssh-doc
2014-07-08 Peter Amstutzmissing paren typo in arvados-bcbio-nextgen.py. refs...
2014-07-08 Peter Amstutzbc-bio script links gemini reference data. refs #2991
2014-07-07 Peter Amstutzadd 'import sys' to arvados-bcbio-nextgen. no issue #
2014-07-07 radhikaMerge branch 'master' into 3140-project-content-tabs
2014-07-07 radhikaMerge branch 'master' into 2380-ssh-doc
2014-07-07 radhikaMerge branch 'master' into 3106-modal-loading-indicator
2014-07-07 Peter AmstutzDefault arvados-bcbio-nextgen pipeline to use freebayes...
2014-07-07 radhikaMerge branch 'master' into 3106-modal-loading-indicator
2014-07-07 Peter Amstutzarvados-bcbio-nextgen writes output now. Put write_dir...
2014-07-07 Peter AmstutzBugfix os.environ() -> os.environ[] no issue #
2014-07-07 Peter AmstutzMerge branch 'bcbio-nextgen' refs #2991
2014-07-07 Peter AmstutzAdd -n cores to run bcbio in parallel on a multicore...
2014-07-07 Peter AmstutzAdd $(node.cores) substitution to run-program, and...
2014-07-07 Peter Amstutzrun-command retry after exception when writing output...
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