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ksahlin / NGSpeciesID

Reference-free clustering and consensus forming of long-read amplicon sequencing
GNU General Public License v3.0
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Update example workflow docs #8

Closed marisalim closed 3 years ago

marisalim commented 3 years ago
marisalim commented 3 years ago

Hi @ksahlin - something's failing with the build, but not sure how to fix. I did notice with local installation of NGSpeciesID that medaka is looking for some updated dependencies. Not sure if this is why the Travis CI build failed.

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
medaka 1.0.3 requires biopython<1.77,>=1.73, but you have biopython 1.78 which is incompatible.
medaka 1.0.3 requires grpcio==1.27.2, but you have grpcio 1.38.0 which is incompatible.
medaka 1.0.3 requires ont-fast5-api==3.0.0, but you have ont-fast5-api 3.3.0 which is incompatible.
medaka 1.0.3 requires pysam==0.15.2, but you have pysam 0.16.0.1 which is incompatible.
ksahlin commented 3 years ago

Thanks for the updates! The problem seems to be that the conda-forge was recently broken (as reported here) I hope they fix it soon. In the meantime I will see if we can get the installation to work without using conda-forge. What causes the problem is this line in the installation:

conda install --yes -c conda-forge -c bioconda medaka==0.11.5 openblas==0.3.3 spoa racon minimap2

I will check so that all the packages medaka==0.11.5 openblas==0.3.3 spoa racon minimap2 are available outside the conda-forge channel.

ksahlin commented 3 years ago

The final solution was not to attempt to remove conda-forge from the install command, but instead, use a newer version of conda in the .travis automatic build. Specifically, specifying wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh instead of wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh (which use Miniconda2).

This would not affect installs for users that follow the instructions in the readme and has an updated conda version (>4.9.2 seems to be safe). However, note that it is not safe to update medaka yet. We need to keep using 0.11.5 as specified in the README installation instructions.