Merck / Merck/BioPhi

Cannot build docker

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Dominant language
Python
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Forks
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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

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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