BD2KGenomics/toil-lib issues and pull requests

#51 - Add logging for each job's disk resources used.

Issue - State: closed - Opened by arkal almost 8 years ago - 1 comment

#51 - Add logging for each job's disk resources used.

Issue - State: closed - Opened by arkal almost 8 years ago - 1 comment

#50 - Remove usages of 'shell=True' in AWSProvisioner

Issue - State: closed - Opened by cket almost 8 years ago - 1 comment

#50 - Remove usages of 'shell=True' in AWSProvisioner

Issue - State: closed - Opened by cket almost 8 years ago - 1 comment

#49 - Add limitBAMsortRAM to STAR

Issue - State: closed - Opened by jvivian almost 8 years ago - 3 comments

#49 - Add limitBAMsortRAM to STAR

Issue - State: closed - Opened by jvivian almost 8 years ago - 3 comments

#48 - Return log.final.out from STAR (resolves #47)

Pull Request - State: closed - Opened by jvivian almost 8 years ago - 3 comments

#48 - Return log.final.out from STAR (resolves #47)

Pull Request - State: closed - Opened by jvivian almost 8 years ago - 3 comments

#47 - Return log.final for STAR alignment

Issue - State: closed - Opened by jvivian almost 8 years ago

#47 - Return log.final for STAR alignment

Issue - State: closed - Opened by jvivian almost 8 years ago

#46 - Move toil.spark to toil_lib.spark (resolves #45)

Pull Request - State: closed - Opened by fnothaft about 8 years ago - 10 comments

#45 - Move Spark service jobs over from toil

Issue - State: closed - Opened by fnothaft about 8 years ago - 1 comment

#44 - Update all docker_call invocations to pass job

Issue - State: closed - Opened by cket about 8 years ago

#44 - Update all docker_call invocations to pass job

Issue - State: closed - Opened by cket about 8 years ago

#43 - Use dockerized s3am (resolves #38)

Pull Request - State: closed - Opened by cket about 8 years ago - 3 comments

#43 - Use dockerized s3am (resolves #38)

Pull Request - State: closed - Opened by cket about 8 years ago - 3 comments

#42 - Fix variable name typo in spark-tools

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

#42 - Fix variable name typo in spark-tools

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

#41 - Add CKCC BAM QC (resolves #40)

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

#41 - Add CKCC BAM QC (resolves #40)

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

#40 - Add QC for CKCC

Issue - State: closed - Opened by jvivian about 8 years ago - 1 comment

#40 - Add QC for CKCC

Issue - State: closed - Opened by jvivian about 8 years ago - 1 comment

#39 - Add bam validator (resolves #37)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 10 comments

#38 - Convert s3am invocations to use the s3am docker image

Issue - State: closed - Opened by hannes-ucsc about 8 years ago
Labels: enhancement

#38 - Convert s3am invocations to use the s3am docker image

Issue - State: closed - Opened by hannes-ucsc about 8 years ago
Labels: enhancement

#37 - Write BAM validator function

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 2 comments

#37 - Write BAM validator function

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 2 comments

#36 - Add `within KeepPairs` (resolves #35)

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

#36 - Add `within KeepPairs` (resolves #35)

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

#35 - Add Within KeepPairs to STAR

Issue - State: closed - Opened by jvivian about 8 years ago

#35 - Add Within KeepPairs to STAR

Issue - State: closed - Opened by jvivian about 8 years ago

#34 - Fix make pypi (resolves #33)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 2 comments
Labels: bug

#33 - make pypi is broken

Issue - State: closed - Opened by jvivian about 8 years ago

#33 - make pypi is broken

Issue - State: closed - Opened by jvivian about 8 years ago

#32 - Add generate_file (resolves #29)

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

#32 - Add generate_file (resolves #29)

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

#31 - Handle post-calling-job fate of containers (resolves #14)

Pull Request - State: closed - Opened by arkal about 8 years ago - 17 comments

#31 - Handle post-calling-job fate of containers (resolves #14)

Pull Request - State: closed - Opened by arkal about 8 years ago - 17 comments

#30 - Add generate_file (resolves #29)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 4 comments
Labels: needs work

#30 - Add generate_file (resolves #29)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 4 comments
Labels: needs work

#29 - Add generate_file

Issue - State: closed - Opened by jvivian about 8 years ago

#28 - Reorder Jenkins build targets; gitignore /bin/ and /s3am/ (resolves #19, resolves #26)

Pull Request - State: closed - Opened by cket about 8 years ago - 2 comments

#28 - Reorder Jenkins build targets; gitignore /bin/ and /s3am/ (resolves #19, resolves #26)

Pull Request - State: closed - Opened by cket about 8 years ago - 2 comments

#27 - `make pypi` fails on jenkins

Issue - State: closed - Opened by cket about 8 years ago - 2 comments

#27 - `make pypi` fails on jenkins

Issue - State: closed - Opened by cket about 8 years ago - 2 comments

#26 - Allow range of Toil versions (resolves #25)

Pull Request - State: closed - Opened by cket about 8 years ago - 4 comments

#26 - Allow range of Toil versions (resolves #25)

Pull Request - State: closed - Opened by cket about 8 years ago - 4 comments

#25 - Setup only allows old version of Toil

Issue - State: closed - Opened by cket about 8 years ago

#25 - Setup only allows old version of Toil

Issue - State: closed - Opened by cket about 8 years ago

#24 - Sporadic NoSuchFileError in processFinishedJob

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 1 comment
Labels: bug

#24 - Sporadic NoSuchFileError in processFinishedJob

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 1 comment
Labels: bug

#23 - Prevent virtualenv from installing latest setuptools (resolves #22)

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

#23 - Prevent virtualenv from installing latest setuptools (resolves #22)

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

#22 - `make pypi` fails with password prompt and None type error

Issue - State: closed - Opened by hannes-ucsc about 8 years ago
Labels: build

#22 - `make pypi` fails with password prompt and None type error

Issue - State: closed - Opened by hannes-ucsc about 8 years ago
Labels: build

#21 - Skip push to PyPi from PRs (resolves #20)

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

#21 - Skip push to PyPi from PRs (resolves #20)

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

#20 - Don't push to PyPi for PR builds

Issue - State: closed - Opened by jvivian about 8 years ago

#20 - Don't push to PyPi for PR builds

Issue - State: closed - Opened by jvivian about 8 years ago

#19 - make prepare creates s3am but it is not in the .gitignore

Issue - State: closed - Opened by arkal about 8 years ago - 7 comments

#19 - make prepare creates s3am but it is not in the .gitignore

Issue - State: closed - Opened by arkal about 8 years ago - 7 comments

#18 - Support BAM realignment (resolves #17)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 5 comments

#18 - Support BAM realignment (resolves #17)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 5 comments

#16 - Added abstract wrapper class (resolves #13)

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

#16 - Added abstract wrapper class (resolves #13)

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

#14 - Implement measures to handle spooky containers

Issue - State: closed - Opened by arkal about 8 years ago

#13 - Add PipelineWrapperBuilder to toil-lib

Issue - State: closed - Opened by nsjake about 8 years ago

#13 - Add PipelineWrapperBuilder to toil-lib

Issue - State: closed - Opened by nsjake about 8 years ago

#11 - Update GATK preprocessing pipeline (resolves #8)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 13 comments

#11 - Update GATK preprocessing pipeline (resolves #8)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 13 comments

#10 - Add vcf manipulation tools (resolves #9)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 9 comments

#10 - Add vcf manipulation tools (resolves #9)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 9 comments

#9 - Add VCF manipulation tools

Issue - State: closed - Opened by jpfeil about 8 years ago

#9 - Add VCF manipulation tools

Issue - State: closed - Opened by jpfeil about 8 years ago

#8 - Update GATK preprocessing pipeline

Issue - State: closed - Opened by jpfeil about 8 years ago

#8 - Update GATK preprocessing pipeline

Issue - State: closed - Opened by jpfeil about 8 years ago

#2 - Added Docker client invocation builder; ability to form pipes (resolves #1)

Pull Request - State: closed - Opened by hannes-ucsc about 8 years ago - 2 comments
Labels: needs work

GitHub / BD2KGenomics/toil-lib issues and pull requests