Open jharenza opened 2 weeks ago
I added ggforce
(required for geom_sina
plots in ALT module) and GSVA
(for MMR pathway enrichment in MSI module) to the Dockerfile. How can I test if it is working?
Added WGCNA
, DGCA
, NOISeq
, sva
packages required for oncoplots
module.
Seems like the build was successfully but I am unable to push it back:
# build
(base) ➜ d3b-hope-cohort-analysis git:(rokita/docker-r4.4) ✗ docker build --platform=linux/amd64 -t pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis:latest .
[+] Building 1606.0s (25/25) FINISHED
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 2.80kB 0.0s
=> [internal] load metadata for docker.io/rocker/tidyverse:4.4.0 0.3s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [ 1/20] FROM docker.io/rocker/tidyverse:4.4.0@sha256:3e72037abda2a32d86021bbe5725e727f2c02233e4072557bc70c1e890e3471b 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 2.79kB 0.0s
=> CACHED [ 2/20] WORKDIR /rocker-build/ 0.0s
=> CACHED [ 3/20] RUN apt-get update 0.0s
=> CACHED [ 4/20] RUN apt-get install -y --no-install-recommends apt-utils dialog 0.0s
=> CACHED [ 5/20] RUN apt-get install -y --no-install-recommends libxt6 bzip2 libmagick++-dev 0.0s
=> CACHED [ 6/20] RUN apt update && apt install -y zlib1g-dev libncurses5-dev libbz2-dev liblzma-dev libcurl4-openssl-d 0.0s
=> CACHED [ 7/20] RUN R -e "install.packages('BiocManager', dependencies=TRUE)" 0.0s
=> CACHED [ 8/20] RUN R -e "BiocManager::install(version = '3.19')" 0.0s
=> CACHED [ 9/20] RUN R -e 'BiocManager::install(c( "Biobase", "BiocManager", "broom", "circlize", "ComplexHeatm 0.0s
=> CACHED [10/20] RUN R -e "remotes::install_github('d3b-center/annoFusedata', ref = '321bc4f6db6e9a21358f0d09297142f6029ac 0.0s
=> CACHED [11/20] RUN R -e "remotes::install_github('clauswilke/colorblindr', ref = '90d64f8fc50bee7060be577f180ae019a9bbbb 0.0s
=> [12/20] RUN R -e "devtools::install_github('andymckenzie/DGCA', dependencies = TRUE)" 199.0s
=> [13/20] RUN apt-get update 10.6s
=> [14/20] RUN apt-get -y --no-install-recommends install python3-pip python3-dev 21.9s
=> [15/20] RUN ln -s /usr/bin/python3 /usr/bin/python 0.2s
=> [16/20] RUN python3 -m pip install --upgrade pip 8.2s
=> [17/20] RUN pip3 install "Cython==0.29.15" "setuptools==46.3.0" "six==1.14.0" "wheel==0.34.2" "num 132.7s
=> [18/20] RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz && tar -zxvf 1222.8s
=> [19/20] RUN wget https://github.com/bedops/bedops/releases/download/v2.4.37/bedops_linux_x86_64-v2.4.37.tar.bz2 && t 7.9s
=> [20/20] ADD Dockerfile . 0.0s
=> exporting to image 2.3s
=> => exporting layers 2.3s
=> => writing image sha256:17133f75f0c1cdd8e3e12a85e597f5642f99b3c4d7defdb67f0dba9422769e34 0.0s
=> => naming to pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis:latest 0.0s
# login
(base) ➜ d3b-hope-cohort-analysis git:(rokita/docker-r4.4) docker login -u rathik
Password:
Login Succeeded
# push
(base) ➜ d3b-hope-cohort-analysis git:(rokita/docker-r4.4) docker push pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis:latest
The push refers to repository [pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis]
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denied: requested access to the resource is denied
Image was built and pushed. Tested relevant modules by re-running them on Docker. All ran without issues.
@jharenza regarding your email for DGCA: I was able to successfully install it using the Dockerfile. Please see my commits. Thanks.
This PR updates the docker image. Closes #103
pull using
docker pull pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis:latest