docker container: resfinder tests fail due to git issue after conda python env added to dockerfile

Here are all the commands I used to download the docker container:

docker pull genomicepidemiology/resfinder:v3-kubernetes  

git clone <https://git@bitbucket.org/genomicepidemiology/pointfinder_db.git> 
git clone -b 4.0 <https://git@bitbucket.org/genomicepidemiology/resfinder.git>  
git clone <https://git@bitbucket.org/genomicepidemiology/disinfinder_db.git> db_disinfinder  

cd resfinder/db_resfinder 
python3 INSTALL.py 
## for each db

I need to keep python2.7 for most of the things I am running locally, so I created a conda environment within the dockerfile to run python3.6. I added this chunk after the line "ENV DEBIAN_FRONTEND noninteractive"

nano dockerfile 

##make python3.6 available via conda in dockerfile
FROM continuumio/miniconda
RUN conda create --name test-env python=3.6  && conda clean -a
RUN conda install -c anaconda git && conda clean -a 
ENV PATH /opt/conda/envs/test-env/bin:$PATH
RUN echo "Make sure python version is proper"
RUN python --version

When I run docker run --rm -v $(pwd):/workdir -v $PF_DB:/db_pointfinder -v $RF_DB:/db_resfinder --entrypoint tests/functional_tests.py resfinder from my resfinder directory, I get the following error message:

ERROR: Could not find a version that satisfies the requirement git (from versions: none)
ERROR: No matching distribution found for git
Traceback (most recent call last):
  File "../run_resfinder.py", line 16, in <module>
    from cge.out.util.generator import Generator
  File "/workdir/cge/out/util/generator.py", line 9, in <module>
    from ..result import Result
  File "/workdir/cge/out/result.py", line 6, in <module>
    from .parserdict import ParserDict
  File "/workdir/cge/out/parserdict.py", line 3, in <module>
    from .valueparsers import ValueParsers
  File "/workdir/cge/out/valueparsers.py", line 3, in <module>
    import dateutil.parser
ModuleNotFoundError: No module named 'dateutil'
EEEE
======================================================================
ERROR: test_on_data_with_just_acquired_resgene_using_blast (__main__.ResFinderRunTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/functional_tests.py", line 74, in test_on_data_with_just_acquired_resgene_using_blast
    check=True)
  File "/opt/conda/envs/test-env/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 ../run_resfinder.py -h' returned non-zero exit status 1.

======================================================================
ERROR: test_on_data_with_just_acquired_resgene_using_kma (__main__.ResFinderRunTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/functional_tests.py", line 153, in test_on_data_with_just_acquired_resgene_using_kma
    check=True)
  File "/opt/conda/envs/test-env/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /workdir/run_resfinder.py -ifq data/test_isolate_01_1.fq data/test_isolate_01_2.fq -o running_test/test2 -s 'Escherichia coli' --min_cov 0.6 -t 0.8 --acquired --db_path_res /workdir/db_resfinder --kmaPath /workdir/cge/kma/kma' returned non-zero exit status 1.

======================================================================
ERROR: test_on_data_with_just_point_mut_using_blast (__main__.ResFinderRunTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/functional_tests.py", line 210, in test_on_data_with_just_point_mut_using_blast
    check=True)
  File "/opt/conda/envs/test-env/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /workdir/run_resfinder.py -ifa data/test_isolate_05.fa -o running_test/test3 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /workdir/db_pointfinder --blastPath /workdir/cge/blastn' returned non-zero exit status 1.

======================================================================
ERROR: test_on_data_with_just_point_mut_using_kma (__main__.ResFinderRunTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/functional_tests.py", line 253, in test_on_data_with_just_point_mut_using_kma
    check=True)
  File "/opt/conda/envs/test-env/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /workdir/run_resfinder.py -ifq data/test_isolate_05_1.fq data/test_isolate_05_2.fq -o running_test/test4 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /workdir/db_pointfinder --kmaPath /workdir/cge/kma/kma' returned non-zero exit status 1.

----------------------------------------------------------------------
Ran 4 tests in 5.091s

FAILED (errors=4)

So the error from the first line is that git isn't there. I have git locally, and I tried integrating it into the dockerfile, but neither approach worked.

I tried running the container anyway with docker run --rm -v $(pwd):/workdir -v $PF_DB:/db_pointfinder -v $RF_DB:/db_resfinder resfinder -o resfinder_out -s "Acinetobacter baumannii" --acquired --point -ifa ../raw_dat/fastas/Acinetobacter_baumannii_ab1_genomic.fna and got the error Error: no module names git in from git import repo, so git does seem to be the issue here.

‌

Is this a local issue? Can you offer any help to make git functional with the dockerfile?

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