Merck / BioPhi

BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.
https://biophi.dichlab.org/
MIT License
131 stars 44 forks source link

Cannot build docker #54

Open Marharyta1995 opened 8 months ago

Marharyta1995 commented 8 months ago

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]