Update Dockerfile

[Jessime]

Hello!

I was wondering if it would be possible to get an updated Dockerfile for tiddit 3.x? I was hoping it might be as simple as:

FROM continuumio/miniconda3

RUN conda config --add channels defaults &&\
    conda config --add channels bioconda &&\
    conda config --add channels conda-forge &&\
    conda config --set channel_priority strict &&\
    conda install -c bioconda tiddit

but when I do this I end up with:

#5 7.839 PackagesNotFoundError: The following packages are not available from current channels:
#5 7.839
#5 7.839   - tiddit
#5 7.839
#5 7.839 Current channels:
#5 7.839
#5 7.839   - https://conda.anaconda.org/bioconda/linux-aarch64
#5 7.839   - https://conda.anaconda.org/bioconda/noarch
#5 7.839   - https://repo.anaconda.com/pkgs/main/linux-aarch64
#5 7.839   - https://repo.anaconda.com/pkgs/main/noarch
#5 7.839   - https://repo.anaconda.com/pkgs/r/linux-aarch64
#5 7.839   - https://repo.anaconda.com/pkgs/r/noarch

presumably because tiddit is currently only build for linux-64 as seen here, which doesn't match the needed architecture?

Alternatively, it may make sense to build from source in the image, depending on what tradeoffs you want to make.

[J35P312]

Hello!
I agree, it would be nice to have an up to date dockerfile; I will see what can be done =P.

But for now, have you tried the bioconda/biocontainers docker image?
You can get it from here:

docker pull quay.io/biocontainers/tiddit:

for more info:

https://bioconda.github.io/recipes/tiddit/README.html

[Jessime]

Thanks for the quick response! A few things:

1. I hadn't seen the quay image, thanks. That gets me what I need. Though, I will note that the image only works on my HPC, not on my M1 macbook. So there's a little more motivation for an updated Dockerfile, haha.
2. quay's not noted in the README. Do you accept PRs? If so, would you be interested in a PR cleaning up the INSTALLATION section of your README? Seems like there's also some out of date stuff there.

[pauline-ng]

I would also like to request an up-to-date Dockerfile. (I want to add some extra commands like bgzip to my tiddit container.)

[J35P312]

I have now updated the dockerfile