Importing samtools on JupyterLab
Hi all,
I am currently working on .cram files that need to run a script that uses samtools via Python. I am aware that this is possible to do on swiss-army-knife, but would heavily prefer the interactive nature of JupyterLab for the purposes of my project.
However, when trying to install or import samtools (and other genomics tools like bcftools and htslib, for that matter), attempts to call these programs return a ‘No such file or directory’ message.
Does anyone know if importing samtools and other tools onto the JupyterLab is a possibility, and if so, how I can do this? Thanks so much for your help.
Comments
1 comment
Hi Kent,
It is possible to install samtools on your jupyterlab instance (similar to how bcftools was installed in this notebook: https://github.com/UK-Biobank/UKB-RAP-Notebooks-Genomics/blob/00dec2a40d954068f674d12a5f4075bd0baf9629/Notebooks/G101_UKB-pipeline-pVCF-to-PLINK.ipynb#L98)
Samtools will only be installed when using the instance. If you want to use samtools on multiple instances it may be useful to use a docker file
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