setting up scRNAseq pigx (can't find environment.yml)

[Anna A Monaco]

Hi,

I am trying to install the PiGx scRNA-seq pipeline via Conda, following the steps on GitHub (https://github.com/BIMSBbioinfo/pigx_scrnaseq):

• Download pigx_scrnaseq source code
  • run:

    git clone https://github.com/BIMSBbioinfo/pigx_scrnaseq.git

• Download and install Anaconda from https://www.anaconda.com/download

Done, works fine, directories and files are there. Then:

Locate the 'environment.yml' file in the source code.

• run:

  conda env create -f environment.yml #provide path to the environment.yml file

• activate the environment:

  source activate pigx_scrnaseq

However, the "environment.yml" file is nowhere to be found... Am I missing something? If the yml file is in the source code, why isn't the path directly stated in the installation guide?

** DISCLAIMER: I am a complete novice to Bioinformatics, so I am sorry if this is a stupid question but I cannot figure it out on my own **

But also, I found I am not the only one to have had this problem: https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/45

Thank you in advance,

Anna

AG Zinzen, BIMSB-MDC

[mail...@gmail.com]

Hello, I also encountered the same issue, do you know how to resolve it?

Thanks!

Zonghao

在 2020年2月14日星期五 UTC-5上午4:58:15，Anna A Monaco写道：