Help needed with CROP-seq / open_pipeline isses

[LJK1991]

Hello epigen,

I am a wetlab cellbiologist with beginner to intermediate coding skills and I am trying setup the CROP-seq pipeline in our laboratory. They use looper and also the open_pipelines repository. sadly I cannot get passed a certain step. Now I'm not sure if this is a problem that has anything to do with the open_pipeline scripts, but i do not know where to ask elsewhere. the #https://github.com/epigen/crop-seq.git is archived and cant create issues there. it is called makeref.py and is making a gtf, STAR index and refFlat of the genome i'm using and the viral genome/gRNA that i want. during this script it calls the a looper config.yaml once. however i get this error (CROPenv) lucask@kolossus:~/crop-seq$ make makeref python src/guides_to_ref.py Traceback (most recent call last): File "src/guides_to_ref.py", line 58, in <module> prj = Project(os.path.join("metadata", "config.yaml")) File "/home/lucask/crop-seq/src/looper/looper/models.py", line 772, in __init__ process_pipeline_interfaces(self.metadata.pipelines_dir) File "/home/lucask/crop-seq/src/looper/looper/models.py", line 376, in process_pipeline_interfaces proto_iface = ProtocolInterface(pipe_iface_location) File "/home/lucask/crop-seq/src/looper/looper/models.py", line 2845, in __init__ self.pipe_iface = PipelineInterface(self.pipe_iface_path) File "/home/lucask/crop-seq/src/looper/looper/models.py", line 2471, in __init__ with open(config, 'r') as f: IOError: [Errno 2] No such file or directory: '/media/draco/lucask/open_pipelines/config/pipeline_interface.yaml' make: *** [makeref] Error 1 the config.yaml https://github.com/epigen/crop-seq/blob/master/metadata/config.yaml is a copy of the original except with my directories. I dont know enough (if anything at all) about looper to exactly understand what i am missing. i'm using an enviroment that should have exactly all the dependancies installed. I do see an atacseq.interface.yaml in the open_pipelines but not one for drop-seq, (the one i will eventually need) I was not sure if this issues stems from the fact that you guys are updating this repository or from me making some mistakes with how i should setup the looper config.yaml Could you help me or give some advice. thank you in advance.

Kind regards, Lucas Kuijpers

P.S. let me know if i need to send more info, or if there is another github/webpage where i should look