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HenrikBengtsson / CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data
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TIPCC: annotationData -> /cbc/data,public/annotationData is broken #27

Closed HenrikBengtsson closed 3 years ago

HenrikBengtsson commented 3 years ago

@ivan108 wrote:

Hi Henrik,

I am trying to run Costello-PSCN-Seq pipeline, the frozen version Stephanie was using before she left.

However, the hardcoded symbolic link

annotationData -> /cbc/data,public/annotationData

doesn't work anymore, giving error "cannot access annotationData: Permission denied".

Could you fix that?

HenrikBengtsson commented 3 years ago

This has been fixed on TIPCC (and therefore also on C4):

$ ls -l /cbc/data,public/annotationData/
total 4
drwxr-xr-x 24 henrik cbc 4096 Jan  8  2020 chipTypes
drwxr-xr-x  7 henrik cbc  152 Feb 29  2016 organisms
ivan108 commented 3 years ago

Hmm, I see that it works for user henrik, but still problem for other users, like jocostello or ismirnov:

ls -l /cbc/data,public/annotationData/
ls: cannot access /cbc/data,public/annotationData/: Permission denied
HenrikBengtsson commented 3 years ago

Oh, this is a problem all the way up at /cbc. I'll have to ping sysadm at this.

HenrikBengtsson commented 3 years ago

Should be fixed now.