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4831: Change ObjectType dropdown label.
[arvados.git]
/
crunch_scripts
/
2014-08-14
Tom Clegg
3551: Merge branch 'master' into 3551-go-layout
tree
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commitdiff
2014-08-14
radhika
Merge branch 'master' into 3112-report-bug
tree
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commitdiff
2014-08-14
Peter Amstutz
Merge branch '3505-virtual-work-dir' refs #3505
tree
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commitdiff
2014-08-14
Peter Amstutz
Merge branch 'master' into 3505-virtual-work-dir
tree
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commitdiff
2014-08-14
Peter Amstutz
3505: tinker with logging
tree
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commitdiff
2014-08-14
Peter Amstutz
3505: Fix typo in run-command
tree
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commitdiff
2014-08-14
Peter Amstutz
3505: Move helper scripts into crunchutil module. ...
tree
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commitdiff
2014-08-13
Tom Clegg
3551: Merge branch 'master' into 3551-go-layout
tree
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commitdiff
2014-08-13
Peter Amstutz
3505: Fixed typo comparison of list against 0 instead...
tree
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commitdiff
2014-08-13
Peter Amstutz
3505: Adjust order of initialization to reflect potenti...
tree
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commitdiff
2014-08-13
Peter Amstutz
Added virtual working directory "task.vwd" option to...
tree
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commitdiff
2014-08-12
radhika
Merge branch 'master' into 3296-user-profile
tree
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commitdiff
2014-08-12
Tom Clegg
Merge branch '3531-sort-jobs-with-pipelines' closes...
tree
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commitdiff
2014-08-12
Peter Amstutz
Fix regular expression in decompress-all.py refs ...
tree
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commitdiff
2014-08-12
Peter Amstutz
Fix syntax error in decompress-all.py refs #3373
tree
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commitdiff
2014-08-12
Peter Amstutz
Merge branch '3373-improve-gatk3-snv-pipeline' closes...
tree
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commitdiff
2014-08-12
Peter Amstutz
3373: Test filename extension before attempting to...
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: split-fastq: Fix loop
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: split-fastq: Fix regex again
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: Fix wrong regex group
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: Fix syntax error in split-fastq
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: more run-command cleanup, global p -> taskp,...
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: Switch run-command to use python logging instead...
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: split-fastq: merge loops to capture both single...
tree
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commitdiff
2014-08-08
Peter Amstutz
3373: decompress-all: cleaned up code a bit. Fail...
tree
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commitdiff
2014-08-07
Peter Amstutz
Merge branch 'master' into 3373-improve-gatk3-snv-pipeline
tree
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commitdiff
2014-08-06
Peter Amstutz
Merge branch 'master' into 3373-improve-gatk3-snv-pipeline
tree
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commitdiff
2014-08-05
Peter Amstutz
Disable chunking
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commitdiff
2014-08-05
Peter Amstutz
Chunking fastq seems to work, but is very slow.
tree
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commitdiff
2014-08-05
Peter Amstutz
arvados.LOCATOR
tree
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commitdiff
2014-08-05
Peter Amstutz
import string
tree
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commitdiff
2014-08-05
Peter Amstutz
Fix syntax error
tree
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commitdiff
2014-08-05
Peter Amstutz
Check for None
tree
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commitdiff
2014-08-05
Peter Amstutz
Working on split-fastq to actually split the fastq...
tree
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commitdiff
2014-08-05
Peter Amstutz
Renamed "job.src" to "job.srcdir", "job.id" to "job...
tree
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commitdiff
2014-08-04
Peter Amstutz
$(link ...) now expects complete path.
tree
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commitdiff
2014-08-04
Peter Amstutz
Merge branch 'master' into 3373-improve-gatk3-snv-pipeline
tree
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commitdiff
2014-08-04
Peter Amstutz
Merge branch '3373-improve-gatk3-snv-pipeline' of git...
tree
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commitdiff
2014-08-04
Peter Amstutz
Simplified collection-merge. Added comments to collect...
tree
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commitdiff
2014-08-04
Peter Amstutz
Works now
tree
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commitdiff
2014-08-04
Peter Amstutz
fix parameters
tree
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commitdiff
2014-08-04
Peter Amstutz
Decompress-all wip
tree
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commitdiff
2014-08-01
Peter Amstutz
Added $(task.outdir) and $(job.src)
tree
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commitdiff
2014-07-30
Peter Amstutz
Fix $(node.cores)
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commitdiff
2014-07-30
Peter Amstutz
str or unicode
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commitdiff
2014-07-30
Peter Amstutz
extra / after dir
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commitdiff
2014-07-30
Peter Amstutz
Better error from glob
tree
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commitdiff
2014-07-30
Peter Amstutz
Pretty print
tree
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commitdiff
2014-07-30
Peter Amstutz
Rearranged exception handling a little more
tree
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commitdiff
2014-07-30
Peter Amstutz
More logging
tree
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commitdiff
2014-07-30
Peter Amstutz
Print traceback on exception
tree
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commitdiff
2014-07-30
Peter Amstutz
Set first task to success
tree
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commitdiff
2014-07-30
Peter Amstutz
import copy
tree
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commitdiff
2014-07-30
Peter Amstutz
.st_mode
tree
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commitdiff
2014-07-30
Peter Amstutz
import stat
tree
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commitdiff
2014-07-30
Peter Amstutz
Fix syntax error
tree
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commitdiff
2014-07-30
Peter Amstutz
Refactored and generalized list expansion, can use...
tree
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commitdiff
2014-07-30
Peter Amstutz
Simpler split-fastq, doesn't try to upload the collecti...
tree
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commitdiff
2014-07-29
Peter Amstutz
Change collection create request
tree
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commitdiff
2014-07-29
Peter Amstutz
Debug manifest format to see why api server is rejecting it
tree
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commitdiff
2014-07-29
Peter Amstutz
debug print manifest_text
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commitdiff
2014-07-29
Peter Amstutz
Left debugging in by accident
tree
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commitdiff
2014-07-29
Peter Amstutz
Same bug, different place
tree
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commitdiff
2014-07-29
Peter Amstutz
Input is "reads" not "input"
tree
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commitdiff
2014-07-29
Peter Amstutz
typo fix get_job_param() -> getjobparam()
tree
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commitdiff
2014-07-29
Peter Amstutz
foreach just refers to other parameter to use as iterat...
tree
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commitdiff
2014-07-29
Peter Amstutz
Added "foreach" to run-command wrapper. Needs testing.
tree
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commitdiff
2014-07-29
Peter Amstutz
Don't split fastq, just organize into directories.
tree
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commitdiff
2014-07-29
Peter Amstutz
Full split-fastq wip
tree
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commitdiff
2014-07-09
radhika
Merge branch 'master' into 3106-modal-loading-indicator
tree
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commitdiff
2014-07-08
Peter Amstutz
Merge branch 'resumable-output-upload'. Adds signal...
tree
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commitdiff
2014-07-08
Peter Amstutz
Actually use the resume cache
tree
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commitdiff
2014-07-08
radhika
Merge branch 'master' into 3203-workbench-tutorial
tree
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commitdiff
2014-07-08
Peter Amstutz
Turns out sys.exit runs finally: blocks.
tree
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commitdiff
2014-07-08
Peter Amstutz
Add debugging
tree
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commitdiff
2014-07-08
Peter Amstutz
Wrong num args
tree
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commitdiff
2014-07-08
Peter Amstutz
SigHandler object
tree
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commitdiff
2014-07-08
Peter Amstutz
Still messing with signals.
tree
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commitdiff
2014-07-08
Peter Amstutz
Fix wrong number of parameters
tree
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commitdiff
2014-07-08
Peter Amstutz
Record signals a different way
tree
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commitdiff
2014-07-08
Peter Amstutz
More work on signal handling
tree
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commitdiff
2014-07-08
Peter Amstutz
Forward signals to process.
tree
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commitdiff
2014-07-08
Peter Amstutz
Use resumable upload writing output in run-command
tree
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commitdiff
2014-07-08
radhika
Merge branch 'master' into 2380-ssh-doc
tree
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commitdiff
2014-07-08
Peter Amstutz
missing paren typo in arvados-bcbio-nextgen.py. refs...
tree
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commitdiff
2014-07-08
Peter Amstutz
bc-bio script links gemini reference data. refs #2991
tree
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commitdiff
2014-07-07
Peter Amstutz
add 'import sys' to arvados-bcbio-nextgen. no issue #
tree
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commitdiff
2014-07-07
radhika
Merge branch 'master' into 3140-project-content-tabs
tree
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commitdiff
2014-07-07
radhika
Merge branch 'master' into 2380-ssh-doc
tree
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commitdiff
2014-07-07
radhika
Merge branch 'master' into 3106-modal-loading-indicator
tree
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commitdiff
2014-07-07
Peter Amstutz
Default arvados-bcbio-nextgen pipeline to use freebayes...
tree
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commitdiff
2014-07-07
radhika
Merge branch 'master' into 3106-modal-loading-indicator
tree
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commitdiff
2014-07-07
Peter Amstutz
arvados-bcbio-nextgen writes output now. Put write_dir...
tree
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commitdiff
2014-07-07
Peter Amstutz
Bugfix os.environ() -> os.environ[] no issue #
tree
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commitdiff
2014-07-07
Peter Amstutz
Merge branch 'bcbio-nextgen' refs #2991
tree
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commitdiff
2014-07-07
Peter Amstutz
Add -n cores to run bcbio in parallel on a multicore...
tree
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commitdiff
2014-07-07
Peter Amstutz
Add $(node.cores) substitution to run-program, and...
tree
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commitdiff
2014-07-07
Peter Amstutz
run-command retry after exception when writing output...
tree
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commitdiff
2014-07-04
Peter Amstutz
Merge branch '2991-job-docker-images' refs #2991
tree
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commitdiff
2014-07-04
Peter Amstutz
Merge branch '2342-run-command-wrapper' refs #2342
tree
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commitdiff
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