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Update Docker Images to run on Sagemaker Studio#229

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dburkhardt merged 119 commits intomasterfrom
docker-jupyter-kernels
Mar 25, 2021
Merged

Update Docker Images to run on Sagemaker Studio#229
dburkhardt merged 119 commits intomasterfrom
docker-jupyter-kernels

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@dburkhardt dburkhardt commented Mar 25, 2021 •
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Submission type

  • This submission adds a new dataset
  • This submission adds a new method
  • This submission adds a new metric
  • This submission adds a new task
  • This submission adds a new Docker image
  • This submission fixes a bug (link to related issue: )
  • This submission adds a new feature not listed above

Testing

  • This submission was written on a forked copy of SingleCellOpenProblems
  • GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull request (include link to passed test: )
  • If this pull request is not ready for review (including passing the "Run Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

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  • This submission follows the guidelines in our Contributing document
  • I have checked to ensure there aren't other open Pull Requests for the same update/change

LuckyMD and others added 30 commits March 16, 2021 12:00
@LuckyMD @scottgigante
added slot to data loader
9d9a1f2
@LuckyMD @scottgigante
added zebrafish batch label
177c142
@LuckyMD @scottgigante
add batch info to the README
7a0e693
@LuckyMD @scottgigante
typo
0fa48ef
@LuckyMD @scottgigante
add info about batch to description
e2b486f
@LuckyMD @scottgigante
update text
1dcd74f
@scottgigante
move PR template
1c40068
@scottgigante
temporarily force ubuntu 18.04
32d2eee
@LuckyMD @scottgigante
fix bug zebrafish uninformative labels
81731db
@LuckyMD @scottgigante
add lab as zebrafish batch covariate
05528ae
@scottgigante
Don't remove s3 contents
0c24e84
@scottgigante
coerce exit code to int
f50089b
@scottgigante
fix pr template
7f4dbe3
@scottgigante
fix link to contributing
ad5dd03
@scottgigante
set upstream on master
25cb86d
@scottgigante
run PR tests on only some types
06551b2
@scottgigante
encourage opening as draft
8d0eb15
@scottgigante
actually block draft PRs
ae41e4b
@scottgigante
still run on push
e489302
@scottgigante
try different syntax
3f5e9d6
@scottgigante
more syntax
1f1c63a
@scottgigante
boolean, not string
f5808b4
@scottgigante
test commit
18e7714
@scottgigante
fix apt
72d7757
@scottgigante
fix apt everywhere
23a20d1
@dburkhardt
Update add sagemaker-user and python SDK
fc5b97a
@dburkhardt
fix syntax
84f6e57
@dburkhardt
Merge branch 'docker-jupyter-kernels' of https://github.com/singlecel…
01f9f81 
…lopenproblems/SingleCellOpenProblems into docker-jupyter-kernels
@dburkhardt
remove -buster
9a58842
@dburkhardt
add buster, change user to root for apt-get update
fc41323
dburkhardt and others added 20 commits March 23, 2021 12:00
@dburkhardt
Merge branch 'master' into docker-jupyter-kernels
6f503b1
@github-actions
pre-commit
703a06b
@scottgigante
Merge branch 'master' into docker-jupyter-kernels
17d37f0
@scottgigante
fix missing variable
7c5a688
@scottgigante
bump version to force rebuild
9584701
@dburkhardt
Fix version for patch
3cd125f
@scottgigante
add details on running nextflow locally
80df042
@scottgigante
Merge branch 'docker-jupyter-kernels' of github.com:singlecellopenpro…
c42866e 
…blems/singlecellopenproblems into docker-jupyter-kernels
@scottgigante
Merge branch 'master' into docker-jupyter-kernels
18a7bf8
@scottgigante
fix dockerfile
f07fe6c
@dburkhardt
change workdir
5ed577e
@dburkhardt
Merge branch 'docker-jupyter-kernels' of https://github.com/singlecel…
ad5112b 
…lopenproblems/SingleCellOpenProblems into docker-jupyter-kernels
@dburkhardt
Start docker build from /
c9138de
@dburkhardt
Fix WORKDIR to /home/$NB_USER
2787beb
@dburkhardt
add troubleshooting.md ci skip
0ab02db
@dburkhardt
Add MELD to python-extras
7c5e695
@olgabot
Remove -resume to always run from scratch
06e29bb
@dburkhardt
Patch parse_nextflow.py BREAKS RESULTS.JSON
85655d9
@dburkhardt
Remove bad fix
7f3c4d0
@dburkhardt
Merge pull request #227 from singlecellopenproblems/olgabot/docker-ju…
d89367f 
…pyter-kernels

Remove -resume and other Nextflow tricks
@dburkhardt dburkhardt requested review from LuckyMD and olgabot March 25, 2021 00:04
LuckyMD
LuckyMD reviewed Mar 25, 2021
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Mostly minor things, but the python-extras requirements.txt install into the r-base docker image is problematic I think.

LuckyMD
LuckyMD approved these changes Mar 25, 2021
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Good from my side now. But i'm not the sagemaker or nextflow expert...

@dburkhardt dburkhardt merged commit 17e1c70 into master Mar 25, 2021
@dburkhardt dburkhardt deleted the docker-jupyter-kernels branch March 25, 2021 17:01
rcannood pushed a commit that referenced this pull request Sep 4, 2024
@dependabot
Bump docker/login-action from 2 to 3 (#229)
86d799a 
Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@v2...v3)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
rcannood pushed a commit that referenced this pull request Sep 4, 2024
@dependabot
Bump docker/login-action from 2 to 3 (#229)
271ed6b 
Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@v2...v3)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Former-commit-id: 86d799a
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@LuckyMD LuckyMD LuckyMD approved these changes

@olgabot olgabot Awaiting requested review from olgabot

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@dburkhardt @LuckyMD @scottgigante @olgabot