aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
Other
163 stars 27 forks source link

Update dockerfile please #322

Closed AmosFong1 closed 2 weeks ago

AmosFong1 commented 3 months ago

The protocol for creating docker image doesn't work. The dockerfile doesn't compile successfully.

git clone https://github.com/aertslab/pySCENIC.git
git clone https://github.com/aertslab/LoomXpy.git
git clone https://github.com/aertslab/pycisTopic.git
git clone https://github.com/aertslab/pycistarget.git
git clone https://github.com/aertslab/scenicplus.git
docker buildx build --platform linux/amd64 -t amosfong1/py_scenicplus:3.11 . -f scenicplus/Dockerfile
[+] Building 4.2s (8/28)                                                                                                                               docker:desktop-linux
 => [internal] load .dockerignore                                                                                                                                      0.0s
 => => transferring context: 2B                                                                                                                                        0.0s
 => [internal] load build definition from Dockerfile                                                                                                                   0.0s
 => => transferring dockerfile: 3.26kB                                                                                                                                 0.0s
 => [internal] load metadata for docker.io/library/python:3.8-slim                                                                                                     0.8s
 => [auth] library/python:pull token for registry-1.docker.io                                                                                                          0.0s
 => CACHED [build-image 1/4] FROM docker.io/library/python:3.8-slim@sha256:c630ae44a7111e582c51b5e728a7f54cf373681fa0e9c2deb1659a95279751fa                            0.0s
 => [internal] load build context                                                                                                                                      0.0s
 => => transferring context: 55.98kB                                                                                                                                   0.0s
 => CANCELED [compile-image  2/20] RUN BUILDPKGS="build-essential         libcurl4-openssl-dev         zlib1g-dev         libfftw3-dev         libc++-dev         git  3.4s
 => ERROR [build-image 2/4] RUN mkdir -p /usr/share/man/man1 &&     apt-get -y update &&     apt-get -y --no-install-recommends install         openjdk-11-jdk         3.4s
------                                                                                                                                                                      
 > [build-image 2/4] RUN mkdir -p /usr/share/man/man1 &&     apt-get -y update &&     apt-get -y --no-install-recommends install         openjdk-11-jdk         procps         bash-completion         curl         libfftw3-dev         less &&     rm -rf /var/cache/apt/* &&     rm -rf /var/lib/apt/lists/*:                                        
0.395 Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB]                                                                                                        
0.443 Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB]                                                                                               
0.443 Get:3 http://deb.debian.org/debian-security bookworm-security InRelease [48.0 kB]                                                                                     
0.809 Get:4 http://deb.debian.org/debian bookworm/main amd64 Packages [8786 kB]                                                                                             
1.674 Get:5 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [12.7 kB]                                                                                     
1.674 Get:6 http://deb.debian.org/debian-security bookworm-security/main amd64 Packages [145 kB]                                                                            
2.455 Fetched 9198 kB in 2s (4279 kB/s)                                                                                                                                     
2.455 Reading package lists...                                                                                                                                              
2.873 Reading package lists...                                                                                                                                              
3.252 Building dependency tree...
3.343 Reading state information...
3.350 E: Unable to locate package openjdk-11-jdk
------
Dockerfile:90
--------------------
  89 |     
  90 | >>> RUN mkdir -p /usr/share/man/man1 && \
  91 | >>>     apt-get -y update && \
  92 | >>>     apt-get -y --no-install-recommends install \
  93 | >>>         openjdk-11-jdk \
  94 | >>>         procps \
  95 | >>>         bash-completion \
  96 | >>>         curl \
  97 | >>>         libfftw3-dev \
  98 | >>>         less && \
  99 | >>>     rm -rf /var/cache/apt/* && \
 100 | >>>     rm -rf /var/lib/apt/lists/*
 101 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c mkdir -p /usr/share/man/man1 &&     apt-get -y update &&     apt-get -y --no-install-recommends install         openjdk-11-jdk         procps         bash-completion         curl         libfftw3-dev         less &&     rm -rf /var/cache/apt/* &&     rm -rf /var/lib/apt/lists/*" did not complete successfully: exit code: 100
AmosFong1 commented 2 weeks ago

I created my own docker file during the new branch