conda installation conflict

[dthoward96]

I'm trying to install medaka into a new conda environment using
conda create -n medaka -c conda-forge -c bioconda medaka
and I'm getting conflicts in the installation of it. Is anyone else having issues with this or a work around for getting it installed into a conda environment?

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                               

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package intervaltree conflicts for:
medaka -> intervaltree[version='>=3.0.0']
Package mappy conflicts for:
medaka -> mappy
Package minimap2 conflicts for:
medaka -> minimap2[version='2.11|2.17']
Package libgcc-ng conflicts for:
medaka -> libgcc-ng[version='>=7.3.0']
Package tensorflow conflicts for:
medaka -> tensorflow[version='1.12.0|1.14.0|>=1.12.2']
Package pysam conflicts for:
medaka -> pysam[version='>=0.15.2']
Package ont-fast5-api conflicts for:
medaka -> ont-fast5-api
Package pyyaml conflicts for:
medaka -> pyyaml==5.1
Package numpy conflicts for:
medaka -> numpy==1.16.1
Package samtools conflicts for:
medaka -> samtools[version='1.3.1|1.9']
Package cffi conflicts for:
medaka -> cffi
Package htslib conflicts for:
medaka -> htslib[version='>=1.3.1,<1.4.0a0|>=1.9,<1.10.0a0']
Package bcftools conflicts for:
medaka -> bcftools[version='1.3.1|1.9']
Package biopython conflicts for:
medaka -> biopython
Package xz conflicts for:
medaka -> xz[version='>=5.2.4,<5.3.0a0']
Package python conflicts for:
medaka -> python[version='>=3.6,<3.7.0a0']
Package zlib conflicts for:
medaka -> zlib[version='>=1.2.11,<1.3.0a0']
Package parasail-python conflicts for:
medaka -> parasail-python
Package whatshap conflicts for:
medaka -> whatshap==0.18
Package bzip2 conflicts for:
medaka -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
Package dill conflicts for:
medaka -> dill
Package h5py conflicts for:
medaka -> h5py==2.7.1
Package keras conflicts for:
medaka -> keras==2.2.4
Package libdeflate conflicts for:
medaka -> libdeflate[version='>=1.0,<1.1.0a0|>=1.3,<1.4.0a0']
Note that strict channel priority may have removed packages required for satisfiability.

[cjw85]

Hi @dthoward96

Some of the packages listed above are no longer used by the current medaka package. I'm wondering whether something is up with your base conda environment. Could you try running:

conda clean --all

From the conda documentation this removes the "index cache, lock files, unused cache packages, and tarballs".

[dthoward96]

I ran that and had it remove everything and I'm still getting package conflicts when trying to create a new environment.

conda create -n medaka -c conda-forge -c bioconda medaka
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                               

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package tensorflow conflicts for:
medaka -> tensorflow[version='1.12.0|1.14.0|>=1.12.2']
Package cffi conflicts for:
medaka -> cffi
Package h5py conflicts for:
medaka -> h5py==2.7.1
Package zlib conflicts for:
medaka -> zlib[version='>=1.2.11,<1.3.0a0']
Package htslib conflicts for:
medaka -> htslib[version='>=1.3.1,<1.4.0a0|>=1.9,<1.10.0a0']
Package whatshap conflicts for:
medaka -> whatshap==0.18
Package numpy conflicts for:
medaka -> numpy==1.16.1
Package python conflicts for:
medaka -> python[version='>=3.6,<3.7.0a0']
Package mappy conflicts for:
medaka -> mappy
Package bzip2 conflicts for:
medaka -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
Package samtools conflicts for:
medaka -> samtools[version='1.3.1|1.9']
Package parasail-python conflicts for:
medaka -> parasail-python
Package intervaltree conflicts for:
medaka -> intervaltree[version='>=3.0.0']
Package keras conflicts for:
medaka -> keras==2.2.4
Package libgcc-ng conflicts for:
medaka -> libgcc-ng[version='>=7.3.0']
Package ont-fast5-api conflicts for:
medaka -> ont-fast5-api
Package pyyaml conflicts for:
medaka -> pyyaml==5.1
Package libdeflate conflicts for:
medaka -> libdeflate[version='>=1.0,<1.1.0a0|>=1.3,<1.4.0a0']
Package biopython conflicts for:
medaka -> biopython
Package xz conflicts for:
medaka -> xz[version='>=5.2.4,<5.3.0a0']
Package pysam conflicts for:
medaka -> pysam[version='>=0.15.2']
Package minimap2 conflicts for:
medaka -> minimap2[version='2.11|2.17']
Package bcftools conflicts for:
medaka -> bcftools[version='1.3.1|1.9']
Package dill conflicts for:
medaka -> dill
Note that strict channel priority may have removed packages required for satisfiability.

[cjw85]

I'm afraid I'm not able to reproduce this error. I'm still unconvinced that conda is finding the correct pacakage metadata; keras, pyyaml, and dill are all things on which medaka has depended on in previous versions but not the current version.

What happens if you run the following?

conda create -n medaka -c conda-forge -c bioconda medaka==0.11.0

[cjw85]

@dthoward96 Have you been able to resolve this issue?