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PennLINC / xcpEngine

Official public repository for the XCP Engine. This tool is deprecated in favor of XCP-D and ASLPrep.
MIT License
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Error with design file #311

Closed nooshinjava closed 4 years ago

nooshinjava commented 4 years ago

I have a very basic question: when I run the xcpengine with docker I get the error as below: Constructing a pipeline based on user specifications ···································································· · [D][/design/design.dsn] INFO: /root/matlab/startup.m does not exist ... creating sed: couldn't edit /design/design.dsn: not a regular file · [I][/scratch] · [C][/cohort/cohort.csv] Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.csv -> read.table Execution halted · [O][/xcpOutput] · [M][Executing serially] ····································································

a3sha2 commented 4 years ago

there is sure docker or singularity binding. can you post the command ?

nooshinjava commented 4 years ago

Thanks! the problem resolved! I needed to change the paths and give permission to folders! Sorry!

bwinsto2 commented 4 years ago

@nooshinjava I know this was a while ago but do you happen to remember what permissions/paths you needed to change? I'm running into the same problem, but I think all my permissions are open...

nooshinjava commented 4 years ago

Hi,

For me it wasn't a path permission problem. I found such command as below which worked for me.

singularity run --cleanenv -B /XCP \ /XCP/simg/xcpEngine-latest.simg \ -d /XCP/designs/fc-36p_spkreg.dsn \ -c /XCP/cohort_file/cohort.csv \ -o /XCP/xcpOutput \ -i /XCP/Work \ -t 1

On Tue, Aug 4, 2020 at 5:53 PM bwinsto2 notifications@github.com wrote:

@nooshinjava https://github.com/nooshinjava I know this was a while ago but do you happen to remember what permissions/paths you needed to change? I'm running into the same problem, but I think all my permissions are open...

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