conda environment error about hic HOT 5 OPEN

Hi @erbon7
Thanks for reporting the issue. Indeed I can reproduce it, but I'm really surprise about it.
I'll try to investigate and come back to you
N

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@erbon7
It seems that installing cooltools from bioconda instead of pip solves the issue.
I'll need to make additional test, to update the environment and make a new release ... which could take some times.

In the meantime, you can for instance, manually update your conda env as follow ;

conda activate work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/
conda install -c bioconda cooltools
conda deactivate

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Note that once your conda env is created (and corrected), you can set up a small config file for the conda cache dir to avoid regenerating the conda each time ...

$ cat conda.conf
conda {
  cacheDir = my_conda_dir
}
$ nextflow  run nf-core/hic -profile test,conda -c conda.conf

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Indeed, with the patch the pipeline runs successfully.
Thanks Nicolas for your fast response and for the tip.

from hic.

@erbon7 It seems that installing cooltools from bioconda instead of pip solves the issue. I'll need to make additional test, to update the environment and make a new release ... which could take some times.

In the meantime, you can for instance, manually update your conda env as follow ;

conda activate work/conda/nf-core-hic-1.3.0-6b228b9d59279339a55b4a54b5df58de/
conda install -c bioconda cooltools
conda deactivate

Hi, I got a similar error, but to install 'cooltools from 'bioconda' doesn't fix it.
Any thoughts about it will be really appreciated.

Core Nextflow options
revision : 1.3.0
runName : thirsty_lamarck
container : nfcore/hic:1.3.0
launchDir : /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq
workDir : /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq/work
projectDir : /home/b/.nextflow/assets/nf-core/hic
userName : b
profile : test,conda
configFiles : /home/b/.nextflow/assets/nf-core/hic/nextflow.config, /media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq/conda_hic.conf

Error executing process > 'tads_insulation (SRR4292758_00 - 1000)'

Caused by:
Process tads_insulation (SRR4292758_00 - 1000) terminated with an error exit status (2)

Command executed:

cooltools diamond-insulation --window-pixels SRR4292758_00_1000_norm.cool 15 25 50 > SRR4292758_00_insulation.tsv

Command exit status:
2

Command output:
(empty)

Command error:
Usage: cooltools [OPTIONS] COMMAND [ARGS]...
Try 'cooltools -h' for help.

Error: No such command 'diamond-insulation'.

Work dir:
/media/b/Bigdata3/Chi/Ales_Cvekl/HiC_fastq/work/4c/66d24e86e4b823228ce8865ec6305e

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

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