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veltenlab / CloneTracer

This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 10x libraries
MIT License
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make_bed job, internet connection error #1

Closed erkinacar5 closed 1 year ago

erkinacar5 commented 1 year ago

Hello! I am trying to run the CloneTracer/nuclear-snv snakemake workflow on a cluster. On our login nodes, we have internet connection, so I managed to install all the missing libraries manually. When I start the job, of course it goes to the worker nodes of the cluster and there is no internet connection on these nodes. Due to this, I am now getting a Bioconductor version validation error. Is there any work around for this?

I am attaching both the error log and the stdout from the cluster job. Please let me know if more information is needed. Thank you in advance! :) lsf.o233886173.txt make_bed.log

sergibeneyto commented 1 year ago

Hello,

sorry for the late reply and thank you for your message.

I modified the Snakemake workflow so that now R scripts do not require installing packages from Bioconductor/CRAN. They are pre-installed in a specific conda environment that gets created before Snakemake submits jobs to the cluster.

Give it a try now, hopefully the problem is solved. You will have to clone the repository again as indicated in the Readme page:

git clone https://github.com/veltenlab/CloneTracer cd CloneTracer/library_processing/nuclear-snv conda env create -f envs/optimized10x.yml conda activate optimized10x

Let me know if the problem persists.

sergibeneyto commented 1 year ago

I will close this issue since it was fixed as you pointed out in issue #2