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 <#123 (comment)>, 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"