pip dependency in Conda env spec causes problem for Docker build?

[kbseah]

Tried to build Docker image after containerzing workflow with snakemake [...] --containerize > Dockerfile

However docker build -t mb-pipeline . command fails when trying to build environment containing pip package pytransaln, during gcc compilation of its pyhmmer dependency.

Submitted PR for Bioconda recipe for pytransaln, which may circumvent this issue

[kbseah]

Error message for failed gcc command in docker build:

128.9       checking whether function 'erfc' is available... no
128.9       generating build/temp.linux-x86_64-cpython-312/libdivsufsort.a from vendor/hmmer/libdivsufsort/divsufsort.c
128.9       generating build/temp.linux-x86_64-cpython-312/vendor/hmmer/libdivsufsort/divsufsort.o from vendor/hmmer/libdivsufsort/divsufsort.c
128.9       creating build/temp.linux-x86_64-cpython-312/vendor
128.9       creating build/temp.linux-x86_64-cpython-312/vendor/hmmer
128.9       creating build/temp.linux-x86_64-cpython-312/vendor/hmmer/libdivsufsort
128.9       gcc -pthread -B /conda-envs/a158841b32a4527881b8fcced1235c5f/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /conda-envs/a158841b32a4527881b8fcced1235c5f/include -fPIC -O2 -isystem /conda-envs/a158841b32a4527881b8fcced1235c5f/include -fPIC -Ibuild/temp.linux-x86_64-cpython-312 -I/conda-envs/a158841b32a4527881b8fcced1235c5f/include/python3.12 -c vendor/hmmer/libdivsufsort/divsufsort.c -o build/temp.linux-x86_64-cpython-312/vendor/hmmer/libdivsufsort/divsufsort.o
128.9       error: command 'gcc' failed: No such file or directory
128.9       [end of output]
128.9
128.9   note: This error originates from a subprocess, and is likely not a problem with pip.
128.9   ERROR: Failed building wheel for pyhmmer
128.9 ERROR: Could not build wheels for pyhmmer, which is required to install pyproject.toml-based projects
128.9
128.9
128.9 failed
128.9
128.9 CondaEnvException: Pip failed