Question: salmon tool syntax error on private galaxy instance
0
gravatar for Guy Reeves
5 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Hi

I installed the salmon tool (Galaxy Version 0.8.2) on to my private instance (galaxy version_major": "17.05").

I downloaded some test datasets from the program homepage and ran them but go this error. I know these files work as I also tried them on usegalay.org and there they worked fine. same datasets working on usegalaxy.org

Would anybody be able to tell me what is going wrong? What could cause the 'syntax error near unexpected token `(''

Cheers

Guy

Fatal error: Exit code 2 () /home/galaxy/galaxy/database/job_working_directory/044/44295/tool_script.sh: line 9: syntax error near unexpected token (' /home/galaxy/galaxy/database/job_working_directory/044/44295/tool_script.sh: line 9:salmon -version > /home/galaxy/galaxy/database/tmp/GALAXY_VERSION_STRING_44295 2>&1; mkdir ./index && mkdir ./output && salmon index --transcripts /home/galaxy/galaxy/database/files/054/dataset_54217.dat --kmerLen 31 --threads "${GALAXY_SLOTS:-4}" --index './index' --type 'quasi' --sasamp 1 && ln -s /home/galaxy/galaxy/database/files/054/dataset_54219.dat ./mate1.fastq && ln -s /home/galaxy/galaxy/database/files/054/dataset_54218.dat ./mate2.fastq && salmon quant --index ./index --mates1 <(zcat ./mate1.fastq) --mates2 <(zcat ./mate2.fastq) --libType "IU" --output ./output --allowOrphans --threads "${GALAXY_SLOTS:-4}" --incompatPrior 1e-20 --gcSizeSamp 1 --biasSpeedSamp 1 --fldMax 1000 --fldMean 200 --fldSD 80 --forgettingFactor 0.65 --maxOcc 200 --maxReadOcc 100 --numBiasSamples 2000000 --numAuxModelSamples 5000000 --numPreAuxModelSamples 1000000 --numGibbsSamples 0 --numBootstraps 0 --vbPrior 0.001'

error software error salmon • 170 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by Guy Reeves1.0k

Do you use something other than bash on that server?

ADD REPLYlink written 5 months ago by Devon Ryan1.8k

[root@XXX ~]# /bin/bash --version GNU bash, version 4.1.2(1)-release (x86_64-redhat-linux-gnu) Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html

we can use other shells like csh manually

[root@XX ~]# csh --version tcsh 6.17.00 (Astron) 2009-07-10 (x86_64-unknown-linux) options wide,nls,dl,al,kan,sm,rh,color,filec

does this answer your question ?

ADD REPLYlink written 5 months ago by Guy Reeves1.0k

Yeah, my presumption had been that something other than bash was being used, thus making the command substitution (<(some command)) not work.

ADD REPLYlink written 5 months ago by Devon Ryan1.8k

Any ideas how I can fix it?

ADD REPLYlink written 5 months ago by Guy Reeves1.0k

No, if you can't reproduce it on the command line then I'm not sure what the real problem is.

ADD REPLYlink written 5 months ago by Devon Ryan1.8k
0
gravatar for Guy Reeves
5 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Are you suggesting that I copy the command line from the admin panel and see if that works?

ADD COMMENTlink written 5 months ago by Guy Reeves1.0k

Yes, exactly.

ADD REPLYlink written 5 months ago by Devon Ryan1.8k
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