| 2014-08-12 |
Peter Amstutz | Merge branch '3373-improve-gatk3-snv-pipeline' closes... |
tree | commitdiff |
| 2014-08-12 |
Peter Amstutz | 3373: Test filename extension before attempting to... |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: split-fastq: Fix loop |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: split-fastq: Fix regex again |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: Fix wrong regex group |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: Fix syntax error in split-fastq |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: more run-command cleanup, global p -> taskp,... |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: Switch run-command to use python logging instead... |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: split-fastq: merge loops to capture both single... |
tree | commitdiff |
| 2014-08-08 |
Peter Amstutz | 3373: decompress-all: cleaned up code a bit. Fail... |
tree | commitdiff |
| 2014-08-07 |
Peter Amstutz | Merge branch 'master' into 3373-improve-gatk3-snv-pipeline |
tree | commitdiff |
| 2014-08-06 |
Peter Amstutz | Merge branch 'master' into 3373-improve-gatk3-snv-pipeline |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | Disable chunking |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | Chunking fastq seems to work, but is very slow. |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | arvados.LOCATOR |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | import string |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | Fix syntax error |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | Check for None |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | Working on split-fastq to actually split the fastq... |
tree | commitdiff |
| 2014-08-05 |
Peter Amstutz | Renamed "job.src" to "job.srcdir", "job.id" to "job... |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | $(link ...) now expects complete path. |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | Merge branch 'master' into 3373-improve-gatk3-snv-pipeline |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | Merge branch '3373-improve-gatk3-snv-pipeline' of git... |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | Simplified collection-merge. Added comments to collect... |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | Works now |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | fix parameters |
tree | commitdiff |
| 2014-08-04 |
Peter Amstutz | Decompress-all wip |
tree | commitdiff |
| 2014-08-01 |
Peter Amstutz | Added $(task.outdir) and $(job.src) |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Fix $(node.cores) |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | str or unicode |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | extra / after dir |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Better error from glob |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Pretty print |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Rearranged exception handling a little more |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | More logging |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Print traceback on exception |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Set first task to success |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | import copy |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | .st_mode |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | import stat |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Fix syntax error |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Refactored and generalized list expansion, can use... |
tree | commitdiff |
| 2014-07-30 |
Peter Amstutz | Simpler split-fastq, doesn't try to upload the collecti... |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Change collection create request |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Debug manifest format to see why api server is rejecting it |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | debug print manifest_text |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Left debugging in by accident |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Same bug, different place |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Input is "reads" not "input" |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | typo fix get_job_param() -> getjobparam() |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | foreach just refers to other parameter to use as iterat... |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Added "foreach" to run-command wrapper. Needs testing. |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Don't split fastq, just organize into directories. |
tree | commitdiff |
| 2014-07-29 |
Peter Amstutz | Full split-fastq wip |
tree | commitdiff |
| 2014-07-09 |
radhika | Merge branch 'master' into 3106-modal-loading-indicator |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Merge branch 'resumable-output-upload'. Adds signal... |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Actually use the resume cache |
tree | commitdiff |
| 2014-07-08 |
radhika | Merge branch 'master' into 3203-workbench-tutorial |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Turns out sys.exit runs finally: blocks. |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Add debugging |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Wrong num args |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | SigHandler object |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Still messing with signals. |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Fix wrong number of parameters |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Record signals a different way |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | More work on signal handling |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Forward signals to process. |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | Use resumable upload writing output in run-command |
tree | commitdiff |
| 2014-07-08 |
radhika | Merge branch 'master' into 2380-ssh-doc |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | missing paren typo in arvados-bcbio-nextgen.py. refs... |
tree | commitdiff |
| 2014-07-08 |
Peter Amstutz | bc-bio script links gemini reference data. refs #2991 |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | add 'import sys' to arvados-bcbio-nextgen. no issue # |
tree | commitdiff |
| 2014-07-07 |
radhika | Merge branch 'master' into 3140-project-content-tabs |
tree | commitdiff |
| 2014-07-07 |
radhika | Merge branch 'master' into 2380-ssh-doc |
tree | commitdiff |
| 2014-07-07 |
radhika | Merge branch 'master' into 3106-modal-loading-indicator |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | Default arvados-bcbio-nextgen pipeline to use freebayes... |
tree | commitdiff |
| 2014-07-07 |
radhika | Merge branch 'master' into 3106-modal-loading-indicator |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | arvados-bcbio-nextgen writes output now. Put write_dir... |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | Bugfix os.environ() -> os.environ[] no issue # |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | Merge branch 'bcbio-nextgen' refs #2991 |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | Add -n cores to run bcbio in parallel on a multicore... |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | Add $(node.cores) substitution to run-program, and... |
tree | commitdiff |
| 2014-07-07 |
Peter Amstutz | run-command retry after exception when writing output... |
tree | commitdiff |
| 2014-07-04 |
Peter Amstutz | Merge branch '2991-job-docker-images' refs #2991 |
tree | commitdiff |
| 2014-07-04 |
Peter Amstutz | Merge branch '2342-run-command-wrapper' refs #2342 |
tree | commitdiff |
| 2014-07-03 |
Tim Pierce | Merge branch '2873-permission-links-ownership' |
tree | commitdiff |
| 2014-07-03 |
Peter Amstutz | fix bwa_index |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | Backed that out, make a symlink to tool-data instead |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | tool-data in work |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | fix sub R1 R2 |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | refer template directly |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | write template |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | open for writing |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | fix config copy |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | fixed syntax error |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | Fixed +x |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | First try at bcbio-nextgen script |
tree | commitdiff |
| 2014-07-02 |
Peter Amstutz | Improve output messages a bit |
tree | commitdiff |
| 2014-07-01 |
Peter Amstutz | fix find |
tree | commitdiff |
| 2014-07-01 |
Peter Amstutz | More clever find |
tree | commitdiff |
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