Install v1.0.0 deepmicrobes

[jayramr]

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[jayramr]

help needed
"ModuleNotFoundError: No module named 'models'" How to specify this module name?

[jayramr]

@BiocondaBot help needed

[daler]

Tons of errors in the log about clobbering paths. E.g.,

ClobberWarning: This transaction has incompatible packages due to a shared path.
packages: defaults/linux-64::tensorflow-base-1.9.0-gpu_py36h6ecc378_0, conda-forge/linux-64::tensorflow-1.9.0-py36_0
path: 'lib/python3.6/site-packages/tensorflow/include/Eigen/src/Eigenvalues/ComplexSchur.h'

So it looks like the defaults channel tensorflow-base is already in the conda-forge package tensorflow. You probably only need the latter.

[jayramr]

You probably only need the latter.

Thanks for your update.
Please advise how to pass this ? Do i need to specify a different version.
I checked on deeplc package yaml, they are using tensorflow , not sure how this succeeds

[daler]

@jayramr looking at the upstream repo, it is not installed as typical python package despite being split into modules. It will not be straightforward to package.

One possible way of getting this working is to to copy over the relevant directories from the source repo into the conda package. However these should not go directly into the bin dir to avoid cluttering it. You will likely need to copy them into share and symlink to that location from bin. You might find some hints in e.g. https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/build.sh.

I'd recommend testing extensively locally before pushing back here.

[dpryan79]

The issue is that this (deepmicrobes) isn't written like a python package. It's just a set of scripts and you need to execute it from within the source so the models directory is in the import path. Can you ask the authors to restructure this a bit into a normal package so something like pip install will work with it? They basically just need a setup.py.

[jayramr]

The issue is that this (deepmicrobes) isn't written like a python package. It's just a set of scripts and you need to execute it from within the source so the models directory is in the import path. Can you ask the authors to restructure this a bit into a normal package so something like pip install will work with it? They basically just need a setup.py.
Thanks @dpryan79 i will request them.