Installation failed / dependencies

[steinbrl]

Hi,

I tried to install ntJoin via bioconda, but it fails with dependencies error. I created an empty environment, so the problem is in the dependencies by themself. I could figure out by manual install, that btllib requires python 3.1, which is not avaible anymore in the conda channels, while the resolver is pointing on a samtools conflict. in the conda channels it starts with python3.4. Do you have any ideas, how I could install ntJoin. I'm working on a HPC cluster with CentOS and an (outdated) Anaconda3 installation.

Best wishes,

Lars

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 samtools conflicts for: pybedtools -> pysam[version='>=0.8.1'] -> samtools[version='1.3.1|1.3|1.3.1.|1.5.|1.6.|1.7.|1.9.*|1.7|>=1.3|>=1.3,<1.4|>=1.4,<1.5|>=1.4.1|>=1.4.1,<1.5'] pybedtools -> samtools btllib -> samtools[version='>=1.19.2,<2.0a0'] samtools[version='>=1.10'] Note that strict channel priority may have removed packages required for satisfiability.

[lcoombe]

Hi @steinbrl,

I'm not totally sure where you are seeing that btllib constraint - btllib does not require python 3.1, in fact, it has available installs for python 3.9 and 3.10.

Could you let me know your full command that you're using in a clean environment (nothing, including python, installed)? Are you ensuring that the conda-forge channel is either supplied with -c or is a high priority in your .condarc (https://github.com/bcgsc/ntJoin?tab=readme-ov-file#installation-instructions)?

Thank you for your interest in ntJoin! Lauren

[steinbrl]

Hi lauren,

thanks for the fast reply. here is the full command and the error.

(base) [steinbrl@leinewr009 /hpc/scratch/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/Neuer Ordner]$ conda create -n ntjoin_test -c bioconda -c conda-forge ntjoin=1.1.4 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 samtools conflicts for: pybedtools -> pysam[version='>=0.8.1'] -> samtools[version='1.3.1|1.3|1.3.1.|1.5.|1.6.|1.7.|1.9.*|1.7|>=1.3|>=1.3,<1.4|>=1.4,<1.5|>=1.4.1|>=1.4.1,<1.5'] samtools[version='>=1.10'] btllib -> samtools[version='>=1.19.2,<2.0a0'] pybedtools -> samtools Note that strict channel priority may have removed packages required for satisfiability.

[lcoombe]

Hi @steinbrl,

Hmm - strange, I tried that exact command on both macOS and linux (centos) on my end, and both were able to resolve the environment just fine. The constraints that it seems to be finding don't seem up-to-date - for example, it installs pysam 0.22.1 and samtools 1.20 just fine for me.

What version of conda are you using? Do you have any channels specified in your .condarc?

If you have access to docker or singularity, another alternative would be to use the quay.io ntJoin docker image (https://quay.io/repository/biocontainers/ntjoin)

[steinbrl]

My Conda version is very outdated (4.7.12), but I can't change this. This is the only version installed on the HPC as an module. It could be, that the problem is located there.

Channels are conda-forge, bioconda, r and main

I tried conda update conda, but it throwed an insane amount of dependency problems, so, I never tried it again. I dont like to destroy all of my environments or recreate them... :)

Docker is not working on our cluster, singularity module is not installed... :(

Thanks for your help!

active environment : base active env location : /project/usr/apps/software/zen2/software/Anaconda3/2019.10 shell level : 1 user config file : /home/leinehome/mh-hannover.local/steinbrl/.condarc populated config files : /home/leinehome/mh-hannover.local/steinbrl/.condarc conda version : 4.7.12 conda-build version : 3.18.9 python version : 3.7.4.final.0 virtual packages : base environment : /project/usr/apps/software/zen2/software/Anaconda3/2019.10 (read only) 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 : /project/usr/apps/software/zen2/software/Anaconda3/2019.10/pkgs /home/leinehome/mh-hannover.local/steinbrl/.conda/pkgs envs directories : /home/leinehome/mh-hannover.local/steinbrl/.conda/envs /project/usr/apps/software/zen2/software/Anaconda3/2019.10/envs platform : linux-64 user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.4 Linux/3.10.0-1160.45.1.el7.x86_64 centos/7.9.2009 glibc/2.17 UID:GID : 1000027254:1000131983 netrc file : None offline mode : False

[lcoombe]

Hi @steinbrl,

It's pretty hard to say for sure what will work, since I can't reproduce the behaviour you are seeing on my end, unfortunately.

My best advice would be to try:

1. Using mamba - sometimes that can be better at resolving dependencies. I am unsure if it would work with a conda install that old, but worth a try.

# in an empty, fresh conda environment:
conda install mamba python=3.9
mamba install -c bioconda -c conda-forge ntjoin=1.1.4

2. You could try installing certain requirements in smaller chunks for the ones that for whatever reason were giving version issues (dependency versions for conda recipe: https://github.com/bioconda/bioconda-recipes/blob/135c13ef93b58e4a71da986d5126b88e3a19f2cf/recipes/ntjoin/meta.yaml).

#Ex:
conda install -c bioconda -c conda-forge 'samtools>=1.10' pybedtools

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in ntJoin!