PacificBiosciences/pypeFLOW issues and pull requests

#56 - slurm command does not use MB, NPROC from config file

Issue - State: open - Opened by hughesdj about 5 years ago

#55 - qsub jobs submission error

Issue - State: closed - Opened by wuxiaopei0509 over 5 years ago - 1 comment
Labels: invalid

#54 - PBS needs jobid for qdel

Issue - State: closed - Opened by pb-cdunn over 6 years ago - 7 comments

#53 - Problem with HPC pro and Falcon

Issue - State: closed - Opened by mictadlo over 6 years ago - 4 comments

#52 - Author: revoer2018 <[email protected]>

Pull Request - State: open - Opened by revoer2018 over 6 years ago - 2 comments
Labels: enhancement

#51 - No git tags for each version

Issue - State: closed - Opened by peterjc over 6 years ago - 3 comments

#50 - add support for SLURM job dependencies to pypeFLOW

Issue - State: closed - Opened by aclum almost 7 years ago - 5 comments
Labels: question

#49 - newly created directories not always available fro remote job

Issue - State: closed - Opened by flowers9 over 7 years ago - 1 comment

#48 - Not able to detect any error

Issue - State: closed - Opened by prince26121991 almost 8 years ago - 5 comments

#47 - Consider running autopep8 to improve readablity

Issue - State: open - Opened by mpkocher almost 8 years ago

#46 - Update out of date example in pypeFLOW/example/PypeTest.py

Issue - State: open - Opened by mpkocher almost 8 years ago - 1 comment

#45 - gc3pie pwatcher adaptor

Issue - State: open - Opened by pb-cdunn about 8 years ago

#44 - Job completion not being detected

Issue - State: open - Opened by hans-vg about 8 years ago - 12 comments

#43 - add missing "path" for `os.path.getmtime`

Pull Request - State: closed - Opened by pb-jchin about 8 years ago

#42 - SLURM uses '-p' instead of '-q' to specify partitions (queues).

Pull Request - State: closed - Opened by bredelings about 8 years ago

#41 - Heartbeat files not being created

Issue - State: closed - Opened by bredelings about 8 years ago - 5 comments

#40 - Bad argument to sbatch with SLURM

Issue - State: closed - Opened by bredelings about 8 years ago - 8 comments

#39 - Drop rdflib/rdfextras/html5lib

Pull Request - State: closed - Opened by pb-cdunn about 8 years ago - 1 comment

#38 - network_based slow for job_type=local

Issue - State: open - Opened by cdunn2001 over 8 years ago - 4 comments

#37 - Problem with network_based pwatcher on OSX

Issue - State: closed - Opened by cdunn2001 over 8 years ago - 20 comments

#36 - Simpler pypeflow

Pull Request - State: closed - Opened by pb-cdunn over 8 years ago - 2 comments

#35 - local WIP for PR28

Pull Request - State: closed - Opened by mhsieh over 8 years ago - 4 comments

#34 - Use job_start.sh, installed with execute perms

Pull Request - State: closed - Opened by pb-cdunn over 8 years ago - 1 comment

#33 - job_start.py must be "executable"

Issue - State: closed - Opened by pb-cdunn over 8 years ago - 1 comment

#32 - Blocking process-watcher

Pull Request - State: closed - Opened by pb-cdunn over 8 years ago - 3 comments

#31 - Create multi-threaded, blocking process-watcher

Issue - State: closed - Opened by pb-cdunn over 8 years ago - 3 comments

#30 - New implementation, with a pwatcher bridge

Pull Request - State: closed - Opened by pb-cdunn over 8 years ago - 1 comment

#29 - FALCON qsub issues (part II)

Issue - State: closed - Opened by StefanoLonardi over 8 years ago - 6 comments

#28 - Added network based heartbeat and log server

Pull Request - State: closed - Opened by flowers9 over 8 years ago - 5 comments

#27 - Ensure that directories exist before qsub

Issue - State: closed - Opened by pb-cdunn over 8 years ago - 5 comments
Labels: bug

#26 - `isSatisfied()` needs to wait and re-try on missing outputs.

Issue - State: closed - Opened by pb-cdunn over 8 years ago - 2 comments

#25 - Drop html5lib, used via rdflib

Issue - State: open - Opened by pb-cdunn over 8 years ago - 2 comments

#24 - Fix 23

Pull Request - State: closed - Opened by pb-cdunn over 8 years ago

#23 - Sometimes, exit file is written late

Issue - State: closed - Opened by pb-cdunn over 8 years ago - 1 comment
Labels: bug

#22 - FALCON qsub issues

Issue - State: closed - Opened by StefanoLonardi over 8 years ago - 12 comments
Labels: question

#21 - Fix an issue with submitting jobs using bsub

Pull Request - State: closed - Opened by yfu over 8 years ago - 1 comment

#20 - DB to track files?

Issue - State: open - Opened by pb-cdunn over 8 years ago - 1 comment

#19 - Fix issues with submitting jobs to Torque

Pull Request - State: closed - Opened by raj76 over 8 years ago - 8 comments

#18 - Two levels of directory hierarchy

Issue - State: open - Opened by pb-cdunn over 8 years ago - 2 comments
Labels: enhancement

#17 - Count successes too, and fail early if none.

Pull Request - State: closed - Opened by pb-cdunn about 9 years ago - 2 comments

#16 - `jobStatusMap` inside `_graphvizDot()` not initialized

Issue - State: closed - Opened by pb-jchin about 9 years ago - 1 comment

#15 - Skip "already done" tasks -- 10x faster restart

Pull Request - State: closed - Opened by pb-cdunn about 9 years ago - 7 comments

#14 - Minor changes

Pull Request - State: closed - Opened by pb-cdunn about 9 years ago