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aicb-ZhangLabs / Venus

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conda install error #5

Closed antoine4ucsd closed 1 year ago

antoine4ucsd commented 1 year ago

hello I am very interested in evaluating Venus for my data (scRNAseq data from persons with HIV) I am trying to set up the venus conda env but I get the an error when running

conda create --name venus --file ${repo_dir}/reference_files/venus_spec-file.txt

the log is attached. would you have any suggestions?

thank you in advance for your help!

venus_conda_install.txt

antoine4ucsd commented 1 year ago

looks like the spec-file is linux specific. do you have an udapted one for mac os? thank you!

Cheyujlee commented 1 year ago

Hi @antoine4ucsd , Thank you for your interest. Currently building one. Thanks! Che Yu.

antoine4ucsd commented 1 year ago

that would be great thank you!

Cheyujlee commented 1 year ago

Hi @antoine4ucsd

Sorry for the delay! Idk if you are working on an ARM64 apple silicon mac, but for me (working on an M1), the problem is that conda doesn't have a lot of Venus's depedencies available for apple silicon just yet. image

Here is the Conda env file for the list of python packages that could be found on Conda:

However, the most important packages you need to manually install and add to $Path:

Last but not least, most importantly, I am going to assume you have at least 30 GB (prob more to be safe) of RAM on your Mac. The reason why STAR Aligner is fast is that it utilizes a lot of memory. The human genome will require 30 GB of RAM. If not, it will take forever to map. For me, my lap top only has 16 GB of RAM.

Sorry again for the 2-wk delay. Hope this helps! Feel free to reply back for any further Q's.

Have a good holiday! CheYu "Joey".

antoine4ucsd commented 1 year ago

thank you. I am also working on a last gen macbook pro. I will give it a try asap Best,