Problem with installation using Docker

[camilagazolla]

Hello,

I am struggling to install inStrain using docker.

(base) camilagazollavolpiano@B005429-NLA docker % make
#yes | cp -a ../common_utils/ ./
#docker image build --no-cache -t instrain:1.7.5  -t instrain:latest -f Dockerfile .
docker image build -t instrain:1.7.5  -t instrain:latest -f Dockerfile .
[+] Building 2231.5s (9/12)                                                                                                                                                                                                             
 => [internal] load build definition from Dockerfile                                                                                                                                                                               0.0s
 => => transferring dockerfile: 807B                                                                                                                                                                                               0.0s
 => [internal] load .dockerignore                                                                                                                                                                                                  0.0s
 => => transferring context: 2B                                                                                                                                                                                                    0.0s
 => [internal] load metadata for docker.io/continuumio/miniconda3:4.6.14                                                                                                                                                           3.7s
 => [internal] load build context                                                                                                                                                                                                  0.0s
 => => transferring context: 23.20kB                                                                                                                                                                                               0.0s
 => [1/8] FROM docker.io/continuumio/miniconda3:4.6.14@sha256:97c73cf6b1aef82bb9f79d9ee82bdcb7bcef07d508fa270bc608bf61d7e98bec                                                                                                   116.2s
 => => resolve docker.io/continuumio/miniconda3:4.6.14@sha256:97c73cf6b1aef82bb9f79d9ee82bdcb7bcef07d508fa270bc608bf61d7e98bec                                                                                                     0.0s
 => => sha256:2a7608a50ae3196483b5426987a8ca4b1564aae8c1305f77d2cd1f14d9e08220 42.05MB / 42.05MB                                                                                                                                  96.7s
 => => sha256:ed7fdbb53a8b0acca9d81343bd711700843e21baea88e3c9ff3df81a5d9f8287 103.68MB / 103.68MB                                                                                                                               114.5s
 => => sha256:97c73cf6b1aef82bb9f79d9ee82bdcb7bcef07d508fa270bc608bf61d7e98bec 1.37kB / 1.37kB                                                                                                                                     0.0s
 => => sha256:6b5cf97566c3b1d8bfd4ff1464fbdaaa9d9737c26d1b153eb3e88358d3826c48 3.71kB / 3.71kB                                                                                                                                     0.0s
 => => sha256:e79bb959ec00faf01da52437df4fad4537ec669f60455a38ad583ec2b8f00498 45.34MB / 45.34MB                                                                                                                                   7.7s
 => => sha256:d9f5448383b9f7a1c5dffd7915eb3b5d28ea2e20fcc500258ab1fae07c8b5bfb 8.44kB / 8.44kB                                                                                                                                     8.3s
 => => extracting sha256:e79bb959ec00faf01da52437df4fad4537ec669f60455a38ad583ec2b8f00498                                                                                                                                          0.6s
 => => sha256:e902202dc40d783b8488c23ccfa62938ff77fa3f9a41cbf61288d567f3708796 8.44kB / 8.44kB                                                                                                                                     9.2s
 => => extracting sha256:2a7608a50ae3196483b5426987a8ca4b1564aae8c1305f77d2cd1f14d9e08220                                                                                                                                          0.5s
 => => extracting sha256:ed7fdbb53a8b0acca9d81343bd711700843e21baea88e3c9ff3df81a5d9f8287                                                                                                                                          1.3s
 => => extracting sha256:d9f5448383b9f7a1c5dffd7915eb3b5d28ea2e20fcc500258ab1fae07c8b5bfb                                                                                                                                          0.0s
 => => extracting sha256:e902202dc40d783b8488c23ccfa62938ff77fa3f9a41cbf61288d567f3708796                                                                                                                                          0.0s
 => [2/8] RUN mkdir -p /mnt                                                                                                                                                                                                        0.3s
 => [3/8] WORKDIR /mnt                                                                                                                                                                                                             0.0s
 => [4/8] RUN conda config --add channels defaults && conda config --add channels bioconda && conda config --add channels conda-forge                                                                                              1.9s
 => ERROR [5/8] RUN conda create -n work -y instrain awscli samtools coverm && conda clean -afy                                                                                                                                 2109.3s 
------                                                                                                                                                                                                                                  
 > [5/8] RUN conda create -n work -y instrain awscli samtools coverm && conda clean -afy:
#0 1.126 Collecting package metadata: ...working... done
#0 286.5 Solving environment: ...working... Killed
------
Dockerfile:15
--------------------
  13 |     
  14 |     #RUN conda install mamba
  15 | >>> RUN conda create -n work -y instrain awscli samtools coverm && conda clean -afy
  16 |     
  17 |     RUN /bin/bash -c "source activate work && \
--------------------
ERROR: failed to solve: process "/bin/sh -c conda create -n work -y instrain awscli samtools coverm && conda clean -afy" did not complete successfully: exit code: 137
make: *** [build] Error 1

It would be really nice to have an option with singularity for using inStrain in HPCs too! :))

[MrOlm]

Hi @camilagazolla -

Apologies- I haven't kept up with maintenance of that Docker. The Singularity and Docker contains I use for inStriain are:

https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0

and

quay.io/biocontainers/instrain

Best, Matt