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'
Do you use something other than
bashon that server?[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 ?
Yeah, my presumption had been that something other than
bashwas being used, thus making the command substitution (<(some command)) not work.Any ideas how I can fix it?
No, if you can't reproduce it on the command line then I'm not sure what the real problem is.