trouble installing pipeline

[l-yampolsky]

snakemake --use-conda -p all --cores 2
Working directory: /Users/levyampolsky/Desktop/BioInfoSoft/NanoporeTools/pipeline-structural-variation-master/results/
Using {sample}/target.bed as target file
KeyError in line 147 of /Users/levyampolsky/Desktop/BioInfoSoft/NanoporeTools/pipeline-structural-variation-master/Snakefile:
'threads'
File "/Users/levyampolsky/Desktop/BioInfoSoft/NanoporeTools/pipeline-structural-variation-master/Snakefile", line 147, in

Any ideas what I might be doing wrong?
Under macOS 10.12.

Thanks!

[arturo-opsetmoen-amador]

Hi,

I am getting a very similar error when trying to install:

snakemake --use-conda -p all Working directory: /home/ubuntu/4_9TB/pipeline_structural_variation/pipeline-structural-variation-1.6.0/results/ Using {sample}/target.bed as target file KeyError in line 148 of /home/ubuntu/4_9TB/pipeline_structural_variation/pipeline-structural-variation-1.6.0/Snakefile: 'threads' File "/home/ubuntu/4_9TB/pipeline_structural_variation/pipeline-structural-variation-1.6.0/Snakefile", line 148, in <module>

[philres]

Hi both,

thanks for reporting. Could you please try adding:

threads: 100

to your config file. That will solve this problem. The nuber (here 100) will be an upper limit. The actual thread number is still controlled by snakemakes -j/--cores. Next release will make sure that is not required anymore.

Sorry about that,
Philipp

[l-yampolsky]

Dear Philipp,

Thanks! That helped, but - next error:

Building DAG of jobs...
Creating conda environment ../env.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /Users/levyampolsky/Desktop/BioInfoSoft/NanoporeTools/pipeline-structural-variation-master/env.yml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound:

• mosdepth

[philres]

Ah sorry, I missed in your initial post that you are on Mac. The pipeline is currently not available on Mac because of this reason. There is no Mac version for mosdepth.

The mosdepth authors have been working on this (brentp/mosdepth#103) but I haven't seen any progress in a while.

Would you be able to run it on a Linux computer?

[l-yampolsky]

I can; however, at the moment I am trying to put together an instructional lab for undergrads (or maybe even high school students), so the idea is to keep everything from basecalling to analysis on a desktop.

Should I try it in Win10? Or is its unix emulator even further away from native linux than MacOS?

[philres]

Good question, haven't tried it with the linux subsytem for Windows.

What about using docker? It's easy to install on a Mac and with a miniconda container (docker run -i -t continuumio/miniconda3 /bin/bash) it should be straight foward to setup the pipeline and run it.

[ATpoint]

I managed to build mosdepth on Mac (10.14.6), see https://www.biostars.org/p/437365/ plus Brent now provides some non-static binaries, brentp/mosdepth#103 (comment)