Closed marisalim closed 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.
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.
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.