YeoLab / YeoLab/containers

Having issues with one of the RUN in the docker file

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@byee4 is already working on this.

Since Jun 7, 2023.

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Description

Hi Brian, I'm having issues with RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt in the docker file. Now I'm just using a copy of deseq2/1.39's files and only added one line in conda-packages.txt file, bioconductor-ensdb.hsapiens.v79.

But when I try to build it, I always encounter issues with the error below:

(base) shuhaoxu@Shuhaos-MBP 1.39.3 % docker build -t deseq2/1.39.3 .
[+] Building 617.1s (10/12)                                                                          
 => [internal] load .dockerignore                                                               0.0s
 => => transferring context: 2B                                                                 0.0s
 => [internal] load build definition from Dockerfile                                            0.0s
 => => transferring dockerfile: 1.62kB                                                          0.0s
 => [internal] load metadata for docker.io/jupyter/datascience-notebook:hub-2.2.2               1.1s
 => [auth] jupyter/datascience-notebook:pull token for registry-1.docker.io                     0.0s
 => [1/7] FROM docker.io/jupyter/datascience-notebook:hub-2.2.2@sha256:f5984966ed1024e70369860  0.0s
 => [internal] load build context                                                               0.0s
 => => transferring context: 825B                                                               0.0s
 => CACHED [2/7] COPY apt-packages.txt /tmp/apt-packages.txt                                    0.0s
 => [3/7] COPY conda-packages.txt /tmp/conda-packages.txt                                       0.0s
 => [4/7] RUN apt-get update && xargs apt-get install -y < /tmp/apt-packages.txt              231.7s
 => ERROR [5/7] RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.t  384.7s 
------                                                                                               
 > [5/7] RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt:             
------                                                                                               
Dockerfile:26                                                                                        
--------------------                                                                                 
  24 |     
  25 |     # Install additional R packages from conda-forge using mamba
  26 | >>> RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt
  27 |     
  28 |     RUN Rscript -e 'install.packages("devtools", repos = "https://cran.us.r-project.org")'
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt" did not complete successfully: exit code: 137

I also tried to just switch using mamda to conda , which did not work neither.

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