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Develop #69

Merged
merged 59 commits into from
Apr 23, 2020
Merged

Develop #69

merged 59 commits into from
Apr 23, 2020

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nikhil
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@nikhil nikhil commented Apr 23, 2020

  • Robustify job submission
  • Improved lsf client
  • Updated Makefile
  • Slight tweaks and bug fixes

stevekm and others added 30 commits January 24, 2020 14:08
@stevekm
add Makefile
ef27d45
@stevekm
add Makefile and sample job fixture
6403c5c
@stevekm
add make superuser to Makefile
9d6d628
@stevekm
update LSF SLA
945e9c5
@stevekm
Merge branch 'develop' into dev-box
cab3211
@stevekm
Merge branch 'develop' into dev-box
7318301
@stevekm
add versions for Postgres and RabbitMq in Makefile
350b1a5
@stevekm
merge against develop
b6d7cfa
@stevekm
add MSKCC Toil install, fix database port env variable in Makefile
8a0e874
@stevekm
update toil to 3.21.0
245db2a
@stevekm
Merge pull request #25 from mskcc/dev-box
86ea3a5 
Dev box
@sivkovic
Revert migrations
f877434
@nikhil
Merge pull request #40 from mskcc/hotfix/migrations
bd3e014 
Hotfix/migrations
@stevekm
update Makefile env settings
a2ae9ec
@stevekm
fix celery worker queue name in Makefile
51e834a
@stevekm
clean up Makefile and settings
c4cb608
@stevekm
Merge pull request #42 from mskcc/fix-dev-box
f342044 
Fix dev box
@stevekm
update Makefile with commands and config to run Singularity instance
6b6808b
@stevekm
change ridgeback_service Singularity container to 18.04
6007a85
@stevekm
add scripts for building Singularity container
49baca5
@sivkovic
version bump for git, sort jobs by created_date, and pep8 fixes
dd683fb
@sivkovic
Merge pull request #48 from mskcc/feature/deploy_fixes
eed36fb 
Version bump of PythonGit
@nikhil
Preserve SINGULARITY_CACHEDIR environment
6e1eaa6
@nikhil
Added batch_system folder for future modularity
134477a 
- Added refactored LSF client with better LSF integration
@nikhil
Removed LSF specific logic from tasks to lsf_client
126170a
@nikhil
Added message in Job model to display job PEND/EXIT/{S,U,P}SUSP messages
dee89a0
@nikhil
[PEP8] Fixed issue with super() format
d134ecb
@nikhil
Merge pull request #49 from mskcc/hotfix/preserve_SINGULARITY_CACHEDIR
7dbebd6 
Preserve SINGULARITY_CACHEDIR environment
@nikhil
A few slight fixes
b460de6
@nikhil
Removing backwards compatability for older version of toil
b716e81
nikhil and others added 26 commits March 10, 2020 14:46
@nikhil
Handle unhandled statuses
5c2cf8a
@nikhil
Set child jobs of non-running leader jobs to status UNKOWN
1d4375a
@nikhil
Updated migrations
a06214d
@nikhil
Added pep8 compliance fixes for lsf_client
11b66ec
@nikhil
Increased version of django
f2e019c
@nikhil
Added missing input type
abe77c0
@nikhil
Merge pull request #53 from mskcc/feature/improve_lsf_client
77a1440 
Feature/improve lsf client
@nikhil
Robustify job submission
a40440d
@nikhil
Slight refactor
2e7d54b
@nikhil
Merge pull request #55 from mskcc/feature/robust_database_handling
18833ed 
Robustify job submission
@nikhil
Fixed variable name after refactor
16dd830
@nikhil
Merge pull request #56 from mskcc/hotfix/fix_variable_name
141ab47 
Fixed variable name after refactor
@nikhil
Ensure that Status is changed only once per iteration
4830d5d
@nikhil
Added job_outputs_dir return value and some pep8 fixes
1381654
@nikhil
Removed unused output_dir model
09114a8 
- Resolves #46
@nikhil
Merge pull request #59 from mskcc/hotfix/fix_status_and_output_dir
aebe621 
Hotfix/fix status and output dir
@nikhil
Added missing migration for removing job output
53c66e9
@nikhil
Merge pull request #60 from mskcc/hotfix/added_missing_migration
bcb9595 
Added missing migration for removing job output
@nikhil
Updated serializer
db99802
@nikhil
Merge pull request #61 from mskcc/hotfix/updated_serializer
b30ee7e 
Updated serializer
@allanbolipata
Removed 'outputs' from job_outputs_dir
cdca817
@allanbolipata
Update jobsubmitter.py
4ba73b9
@allanbolipata
Merge pull request #62 from mskcc/feature/remove_output_string
7293fa6 
Removed 'outputs' from job_outputs_dir
@stevekm
remove Singularity recipe and update build recipe
77d4336
@stevekm
add help to container Makefile
6f0e28d
@stevekm
Merge pull request #44 from mskcc/makefile-singluarity
0f5137f 
update Makefile with commands and config to run Singularity instance
allanbolipata
allanbolipata approved these changes Apr 23, 2020
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Looks good. Let's make an official release, too

@nikhil nikhil merged commit e97846b into master Apr 23, 2020
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@allanbolipata allanbolipata allanbolipata approved these changes

@sivkovic sivkovic Awaiting requested review from sivkovic

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4 participants
@nikhil @allanbolipata @stevekm @sivkovic