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epigen / crop-seq

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
https://crop-seq.computational-epigenetics.org
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Setting up Looper and pipelines #1

Closed weizhiting closed 7 years ago

weizhiting commented 7 years ago

Hi! when i run this command 'make makeref' command, i got an error. Indeed,it caused by this prj = Project(os.path.join("metadata", "config.yaml")),Could you help me! Moreover,in the config.yaml,what does the pipelines_dir refer to?Thanks!

afrendeiro commented 7 years ago

Hello!

This repository used the project management system Looper to handle the project, but also to process the raw data. You can read here more on it and how to set it up.

I don't know what error you got, but for the project management part you have to have looper installed: e.g. pip install --user https://github.com/epigen/looper/zipball/master. To make sure all requirements are satisfied you can run make requirements which will try to get all requirements from requirements.txt.

If you want to process the raw data you have to have additionally a looper-compatible pipeline repository like this one where you'll find the Drop-seq pipeline I used to process the data (this in addition has its own requirements), but since this is perhaps a bit complex I recommend you just get the processed data from GEO if your intention is to play with it.

weizhiting commented 7 years ago

Hi! Thanks! I will try what you said!

afrendeiro commented 7 years ago

Please feel free to reopen the issue if more problems arise.