docker build failing

[ekg]

I'm unable to build using docker:

erik@copito [01:10:50 PM] [~/blobtools] [master]
-> % docker build -t drl/blobtools . 

This crashes and burns:

Collecting package metadata (repodata.json): ...working... done

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - pysam -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  - python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

I actually tried docker because I got the exact same error when building in a conda environment. It looks like something has gone wrong in bioconda's dependencies?

[ywxue00]

@ekg Hello, how did this error of yours finally solve, I also encountered the same error. Looking forward to your response.

[ekg]

I did not solve it.

On Thu, Apr 6, 2023, 11:45 ywxue00 @.***> wrote:

@ekg https://github.com/ekg Hello, how did this error of yours finally solve, I also encountered the same error. Looking forward to your response.

— Reply to this email directly, view it on GitHub https://github.com/DRL/blobtools/issues/123#issuecomment-1498780446, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEJXWDDWQE22L6T5ZNTW72GDBANCNFSM6AAAAAAQQ63Y2M . You are receiving this because you were mentioned.Message ID: @.***>

[edwardbirdlab]

By changing from conda to pip in the Dockerfile, I was able to successfully install the requirements and get the container working. Incase anyone runs into the same issue my docker File looks like this:

FROM continuumio/miniconda3

RUN conda install -c anaconda matplotlib docopt tqdm wget pyyaml git

RUN conda install -c bioconda pysam --update-deps

RUN git clone https://github.com/DRL/blobtools.git WORKDIR blobtools RUN pip install -r requirements.txt RUN ./blobtools -h

RUN ./blobtools create -i example/assembly.fna -b example/mapping_1.bam -t example/blast.out -o example/test

RUN wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz -P data/ RUN tar zxf data/taxdump.tar.gz -C data/ nodes.dmp names.dmp RUN ./blobtools nodesdb --nodes data/nodes.dmp --names data/names.dmp ENV PATH="$PATH:/blobtools"