Update Battenberg `v2.2.9` Dockerfile #9

Faizal-Eeman · 2023-05-25T18:45:40Z

Description

Standardize Dockerfile and update Battenberg v2.2.9

Closes #1

Closes #2

Testing Results

Docker Image Testing

I have tested the Docker image with the docker run command as described below.

Test the Docker image with at least one sample. Verify the new Docker image works using:

docker run --rm -u $(id -u):$(id -g) -w=`pwd` --volume=/hot/:/hot/ \
    -v /hot/ref/tool-specific-input/Battenberg/download_202204/GRCh38/battenberg_ref_hg38_chr/:/opt/battenberg_reference/ battenberg:2.2.9 \
    Rscript /usr/local/bin/battenberg_wgs.R \
        -t $tumor_sample_name \
        -n $normal_sample_name \
        --nb $normal_bam \
        --tb $tumor_bam \
        -o $sample_out_dir \
        --sex male

Note: The sex of the sample was arbitrarily assigned to test the docker run.

My command:

Battenberg docker command was wrapped in an sbatch shell script and run on an F32.
sbatch /hot/user/mmootor/temp_files/battenberg/run/test_run_battenberg.sh
Log:

/hot/user/mmootor/temp_files/battenberg/run/battenberg.error
/hot/user/mmootor/temp_files/battenberg/run/battenberg.log

Test Cases

Case 1
- sample: ILHNLNEV000009-N001-B01-F , ILHNLNEV000009-T002-L01-F
- normal: /hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/pipelines/call-gSNP/2020-12-22/ILHNLNEV000009-T002-L01-F//gSNP/2021-01-22_11.01.06/ILHNLNEV000009/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000009-N001-B01-F_realigned_recalibrated_reheadered.bam
- tumor: /hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/pipelines/call-gSNP/2020-12-22/ILHNLNEV000009-T002-L01-F//gSNP/2021-01-22_11.01.06/ILHNLNEV000009/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000009-T002-L01-F_realigned_recalibrated_reheadered.bam
- sbatch: /hot/user/mmootor/temp_files/battenberg/run/test_run_battenberg.sh
- output: /hot/user/mmootor/temp_files/battenberg/run/ILHNLNEV000009-T002-L01-F_subclones.txt
- Germline plot: /hot/user/mmootor/temp_files/battenberg/run/ILHNLNEV000009-T002-L01-F.germline.png
- Tumor plot: /hot/user/mmootor/temp_files/battenberg/run/ILHNLNEV000009-T002-L01-F.tumour.png

Checklist

Formatting

I have read the code review guidelines and the code review best practice on GitHub check-list.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.

File Updates

I have ensured that the version number update follows the versioning standards.
I have updated the version number in the Dockerfile, README.md and metadata.yaml files.
I have updated the dependencies and added my name to the maintainer list in the Dockerfile.
I have updated the feature changes in the README.md (optional).
I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

GitHub Packages Auto Build Rules

I have not manually pushed this Docker image to the uclahs-cds container registry (ghcr.io/uclahs-cds) on GitHub.
I have updated the image_name in the metadata.yaml which is required by GitHub action to automatically build and push the image.

…GRCh37 and GRCh38)

Faizal-Eeman · 2023-05-25T18:53:00Z

I'll create /hot/software/image/docker-Battengberg after we release this docker image and move all relevant logs and test results to the dev dir of this repo.

yashpatel6

Some comments:

Dockerfile

README.md

Dockerfile

modify_reference_path.sh

Faizal-Eeman · 2023-06-08T00:38:33Z

Tested the image again, all works good.
Any other comments? @tyamaguchi-ucla @yashpatel6

Faizal-Eeman · 2023-06-12T18:28:26Z

Did you want to specify the ASCAT version here?

Image tested with ASCAT version specified. Test was successful. Test location same as before.

tyamaguchi-ucla

Added a few minor comments but otherwise, looks good to me. Anything else to add @yashpatel6 ?

tyamaguchi-ucla · 2023-06-12T20:58:47Z

Dockerfile

+ARG HTSLIB_VERSION=1.16
+ARG ALLELECOUNT_VERSION=4.3.0
+ARG IMPUTE2_VERSION=2.3.2
+RUN mamba create -qy -p /usr/local \
+    -c bioconda \
+    -c conda-forge \
+    htslib==${HTSLIB_VERSION} \
+    cancerit-allelecount==${ALLELECOUNT_VERSION} \
+    impute2==${IMPUTE2_VERSION}


No need to worry about this in this PR but we may want to consider creating an image for each tool.

@Faizal-Eeman can you create a GH issue on this?

Issue #12 created.

Dockerfile

yashpatel6

Looks fine to me, agreed on Taka's comment about trying to have fewer layers

yashpatel6 · 2023-06-12T22:33:17Z

Dockerfile

+RUN R -q -e 'devtools::install_github("Crick-CancerGenomics/ascat/[email protected]")'
+
+# Install Battenberg 2.2.9
+RUN R -q -e 'devtools::install_github("Wedge-Oxford/[email protected]")'


We might also want to make ASCAT and Battenberg versions args rather than hard-coded here

Seems to take a bit of dirty work to use ARG here as there are both single and double quotes. I'll update this in another PR later.

Faizal-Eeman · 2023-06-27T18:26:08Z

Reduced layers, verified the image with a successful test run.

Mootor added 9 commits February 23, 2023 14:24

Update Dockerfile for Battenberg 2.2.9 - initial code

46e53cb

use mamba one-liner to install htslib, allelecount and impute2

cecf794

remove redundant codes

d1b0c8a

merge main into current branch

6f61fa3

Standardize resource path modification in Dockerfile (applicable for …

e3eff9b

…GRCh37 and GRCh38)

modify resource file paths

42fc105

Update README.md

bd969d0

Update CHANGELOG.md

1f7a1b2

Update metadata.yaml

8715e8c

Faizal-Eeman requested review from tyamaguchi-ucla and yashpatel6 May 25, 2023 18:49

yashpatel6 reviewed May 25, 2023

View reviewed changes

Mootor added 3 commits May 26, 2023 20:42

add reference path modification script

2d96044

clean up Dockerfile

ef1fe14

add dependencies tool version

5e8a6a4

Faizal-Eeman requested a review from yashpatel6 May 27, 2023 03:52

Update README.md

e52dd02

tyamaguchi-ucla reviewed May 27, 2023

View reviewed changes

Dockerfile Outdated Show resolved Hide resolved

Dockerfile Outdated Show resolved Hide resolved

Dockerfile Outdated Show resolved Hide resolved

modify_reference_path.sh Outdated Show resolved Hide resolved

Mootor and others added 5 commits May 31, 2023 13:55

change i/o varianble names

90bf9d3

install devtools and its dependencies

53dee7d

add r-cran-curl

9a78916

clean up dockerfile

1bc183a

Update CHANGELOG.md

1c0f352

Faizal-Eeman requested a review from tyamaguchi-ucla June 8, 2023 00:37

add ASCAT version

15137ac

tyamaguchi-ucla approved these changes Jun 12, 2023

View reviewed changes

yashpatel6 reviewed Jun 12, 2023

View reviewed changes

reduce layers

e01e551

Faizal-Eeman merged commit ee2a4a0 into main Jun 27, 2023

Faizal-Eeman deleted the mmootor-update-battenberg-2-2-9-dockerfile branch June 27, 2023 19:14

This was referenced Jun 27, 2023

Release docker-Battenberg v2.2.9 #11

Merged

Use multi-stage build for major dependencies #12

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update Battenberg `v2.2.9` Dockerfile #9

Update Battenberg `v2.2.9` Dockerfile #9

Faizal-Eeman commented May 25, 2023 •

edited

Loading

Faizal-Eeman commented May 25, 2023

yashpatel6 left a comment

Faizal-Eeman commented Jun 8, 2023

Faizal-Eeman commented Jun 12, 2023

tyamaguchi-ucla left a comment

tyamaguchi-ucla Jun 12, 2023

tyamaguchi-ucla Jun 27, 2023

Faizal-Eeman Jun 27, 2023

yashpatel6 left a comment

yashpatel6 Jun 12, 2023

Faizal-Eeman Jun 27, 2023

Faizal-Eeman commented Jun 27, 2023

Update Battenberg v2.2.9 Dockerfile #9

Update Battenberg v2.2.9 Dockerfile #9

Conversation

Faizal-Eeman commented May 25, 2023 • edited Loading

Description

Closes #1

Closes #2

Testing Results

Docker Image Testing

Test the Docker image with at least one sample. Verify the new Docker image works using:

My command:

Test Cases

Checklist

Formatting

File Updates

GitHub Packages Auto Build Rules

Faizal-Eeman commented May 25, 2023

yashpatel6 left a comment

Choose a reason for hiding this comment

Faizal-Eeman commented Jun 8, 2023

Faizal-Eeman commented Jun 12, 2023

tyamaguchi-ucla left a comment

Choose a reason for hiding this comment

tyamaguchi-ucla Jun 12, 2023

Choose a reason for hiding this comment

tyamaguchi-ucla Jun 27, 2023

Choose a reason for hiding this comment

Faizal-Eeman Jun 27, 2023

Choose a reason for hiding this comment

yashpatel6 left a comment

Choose a reason for hiding this comment

yashpatel6 Jun 12, 2023

Choose a reason for hiding this comment

Faizal-Eeman Jun 27, 2023

Choose a reason for hiding this comment

Faizal-Eeman commented Jun 27, 2023

Update Battenberg `v2.2.9` Dockerfile #9

Update Battenberg `v2.2.9` Dockerfile #9

Faizal-Eeman commented May 25, 2023 •

edited

Loading