Cannot build docker
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- Dominant language
- Python
- Stars
- 265
- Forks
- 65
- PR merge metrics
- No merged PRs in 30d
Description
I am trying to run the dev server using the instructions for development using docker compose. Once I try to build docker it fails at the stage => ERROR [biophi-main-web 6/9] RUN make env-update ENV_NAME=base with following error:
#0 0.237 conda env update -n base -f environment.yml
#0 0.718 Collecting package metadata (repodata.json): ...working... done
#0 46.40 Solving environment: ...working... failed
#0 46.40
#0 46.40 ResolvePackageNotFound:
#0 46.40 - hmmer[version='>=3.1']
#0 46.40
#0 49.63 make: *** [Makefile:12: env-update] Error 1
I am also not able to install this package locally using Conda, as the package cannot be found (I specify bioconda as a source)
I thought that the problem is in hmmer package so I have downloaded its 3.1 version, located it in the BioPhi directory and added the installation to the docker file. This solved the hmmer problem but raised a lot of package incompatibility errors, which eventually leads to the same results -> docker fails to build. Is there a workaround how to make it work? Thanks a lot for any help.
P.S This is just a small part of error messages I receive:
[worker 8/10] RUN make env-update ENV_NAME=base:
0.108 conda env update -n base -f environment.yml
0.528 Collecting package metadata (repodata.json): ...working... done
27.19 Solving environment: ...working...
54.07 Found conflicts! Looking for incompatible packages.
54.07 This can take several minutes. Press CTRL-C to abort.
Examining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver truststore idna conda cffi conda-content-trust pluggy requests pycosat pysocks tk conda-package-streaming pyopenssl jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml urllib3 anarci pip setuptools certifi abnumber conda-package-handling tqdm pythExamining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver truststore idna conda cffi conda-content-trust pluggy requests pycosat pysocks conda-package-streaming pyopenssl jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml urllib3 anarci pip setuptools certifi abnumber conda-package-handling tqdm python Examining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver truststore idna conda cffi conda-content-trust pluggy requests pycosat pysocks conda-package-streaming pyopenssl jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml urllib3 anarci pip setuptools certifi abnumber conda-package-handling tqdm python Examining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver pcre2 truststore idna conda cffi conda-content-trust pluggy libarchive requests bzip2 pycosat pysocks conda-package-streaming pyopenssl libmamba jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml libsolv urllib3 anarci pip setuptools certifi abnuExamining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver pcre2 truststore idna conda cffi conda-content-trust pluggy libarchive requests bzip2 pycosat pysocks conda-package-streaming pyopenssl libmamba jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml libsolv urllib3 anarci pip setuptools certifi abnuExamining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver readline truststore idna conda cffi conda-content-trust pluggy requests pycosat krb5 pysocks conda-package-streaming sqlite pyopenssl ncurses jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml urllib3 anarci pip setuptools certifi abnumber conda-Examining conflict for pycparser packaging brotlipy charset-normalizer conda-libmamba-solver readline truststore idna conda cffi conda-content-trust pluggy requests pycosat krb5 pysocks conda-package-streaming sqlite pyopenssl ncurses jsonpatch libmambapy wheel cryptography jsonpointer zstandard ruamel.yaml urllib3 anarci pip setuptools certifi abnumber conda-Examining conflict for conda-package-streaming zstandard pycparser brotlipy urllib3 conda anarci charset-normalizer pip setuptools requests certifi jsonpatch abnumber wheel conda-package-handling cryptography jsonpointer: 7%|▋ | 5/76 [00:02<00:28, 2.48it/s]
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the Dockerfile stage that runs make env-update, then inspect Makefile and environment.yml for the hmmer >=3.1 dependency and Conda channels. Reproduce the Docker Compose build and determine a dependency configuration that resolves successfully; done means the image builds without the reported package-not-found or incompatibility errors.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- anaconda, docker, docker-compose, python
- Domain
- build-system, devops
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100