CONFIG ERROR:Cannot access config file (/var/pipeline/ref/GRCm38.p6/GRCm38.bammatcher_docker.conf).

roland-rad-lab / MoCaSeq

Analysis pipelines for cancer genome sequencing in mice.

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CONFIG ERROR:Cannot access config file (/var/pipeline/ref/GRCm38.p6/GRCm38.bammatcher_docker.conf). #15

Open geng-lee opened 1 year ago

geng-lee commented 1 year ago

Hi,

I've tried running the MoCaSeq pipeline multiple times, but each time I get a CONFI G ERROR. Could you help me about this problem ?

Thanks!

22526424.log

+--------------+ | CONFIG ERROR | +--------------+ Cannot access config file (/var/pipeline/ref/GRCm38.p6/GRCm38.bammatcher_docker.conf). It either does not exist or is not readable.

best, jamie

NikdAK commented 1 year ago

Hi, did you install git LFS before pulling? Some larger files are not downloaded without LFS.

Anyways, you can find that file in the data/ folder in this repo, so you could manually download it.

geng-lee commented 1 year ago

I didn't notice if git LFS was installed, but I found that GRCm38.bammatcher_docker.conf is in my ref directory (ref/GRCm38.p6/GRCm38.bammatcher_docker.conf), not /var/pipeline/ref/GRCm38.p6/. How can I solve this problem？

Thanks!