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BIMSBbioinfo / pigx_scrnaseq

Pipeline for analysis of Dropseq single cell data
http://bioinformatics.mdc-berlin.de/pigx
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environment.yml file missing for conda installation #45

Closed davisidarta closed 4 years ago

davisidarta commented 5 years ago

Hello there Pigx team!

I'm a junior bioinformatician in charge of our research group analysis and I'd like to test Pigx for analyzing some Fastq files for RNA velocity estimation (I was originally going to use DropSeq pipeline). However, I'm having some issues installing it, since GNU Guix installation was troublesome on our HPC cluster.

I then proceeded to try to install via conda. However, the environment.yml file is missing from the git source when installed by (git clone https://github.com/BIMSBbioinfo/pigx_scrnaseq.git). I need it to run conda env create -f environment.yml and proceed through conda installation of Pigx.

Any chance this can receive an update?

Cheers!

rekado commented 4 years ago

We don't recommend the use of Conda. For reproducibility we recommend using Guix.

We could however welcome a patch / pull request to add environment.yml.