export2graphlan with biom-format

[Midnighter]

I'm trying to use export2graphlan with biom-format support which is turning out to be a bit tricky. On one hand, the biocontainer quay.io/biocontainers/export2graphlan:0.22--py_0 is a Python 2.7 image which doesn't have an obvious way to install build tools which would be required for compiling biom-format. Also conda seems to be disabled. On the other hand, I can add export2graphlan.py locally to a biom-format image, for example, biocontainers/biom-format-v2.1.7dfsg-2-deb-py2_cv1.

However, it is very unclear to me where to suggest creating an image that includes both. Should I go to the bioconda export2graphlan recipe? Which seems to be the source for the biocontainer? Should I suggest a new biocontainer? Should I somehow create a mulled container? I'm a bit new to biocontainers and confused. Thank you for any pointers.

[osallou]

Hi, Mulled based containers from conda only contain tool and nothing and cannot be indeed easily extended (quai.io containers) If you take a docker based container you are on a debian/ubuntu base so you can install additional packages using apt-get, conda etc...

For a oneshot or alike i would sugest you take biomformay container whuch is debian based and add scripts you need. After that you can also create a new container to be shared with others