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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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new problem installing phyloflash #153

Closed pacificasommers closed 3 years ago

pacificasommers commented 3 years ago

Hi, I am having an issue installing phyloflash using the recommended approach in conda.

When I used the recommended approach (including from the previous installation issue) of creating an environment simultaneous with installing phyloflash (with or without sortmeRNA at the same time), conda create -n pf sortmerna=2.1b phyloflash, conda just hangs in solving the environment, even when I have set channel priority to strict. (I get the same behavior when they're set to flexible, for what it's worth.)

When I instead tried first creating an environment and then installing just conda using conda install -c bioconda/label/cf201901 phyloflash again with channel priority set to strict, I at least got the environment to solve, but the installation failed due to finding conflicts, but after searching for what they were, reporting only: "UnsatisfiableError: Note that strict channel priority may have removed packages required for satisfiability."

It doesn't tell me what packages may have been missing for satisfiability, so I am unable to diagnose if there is something else I can add or change? My searching online to resolve this as a broader issue hasn't yielded any help yet.

Repeating this attempt to install while already in the environment but with channels set to flexible leads again to conda hanging in solving the environment.

Any ideas on how to proceed?

Details on my lab server and conda environment:

System: Ubuntu 16.04.7 LTS Conda version: conda 4.10.0 Python version: 2.7.12

My conda config: conda config --show-sources ==> /home/pacifica/.condarc <== auto_activate_base: False channel_priority: strict channels:

My conda environment: conda info active environment : pf active env location : /home/pacifica/.conda/envs/pf shell level : 1 user config file : /home/pacifica/.condarc populated config files : /home/pacifica/.condarc conda version : 4.10.0 conda-build version : not installed python version : 3.8.5.final.0 virtual packages : linux=4.4.0=0 glibc=2.23=0 unix=0=0 archspec=1=x86_64 base environment : /ResearchSoftware/miniconda3 (read only) conda av data dir : /ResearchSoftware/miniconda3/etc/conda conda av metadata url : https://repo.anaconda.com/pkgs/main channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /ResearchSoftware/miniconda3/pkgs /home/pacifica/.conda/pkgs envs directories : /home/pacifica/.conda/envs /ResearchSoftware/miniconda3/envs platform : linux-64 user-agent : conda/4.10.0 requests/2.24.0 CPython/3.8.5 Linux/4.4.0-210-generic ubuntu/16.04.7 glibc/2.23 UID:GID : 1002:1002 netrc file : None offline mode : False

kbseah commented 3 years ago

I'm sorry to hear about this issue, it appears to be a problem with Conda.

It may help to try using Mamba instead (drop in substitute for Conda): https://mamba.readthedocs.io/en/latest/

pacificasommers commented 3 years ago

I had not heard of Mamba before - thanks for the suggestion! I got PhyloFlash installed now!