OSX: importFromIMGT.sh: line 40: syntax error near unexpected token `('

[marcovth]

OSX 10.10.5 and OSX 10.11.3 give the same error ...

sh ./importFromIMGT.sh By using this script you agree to the terms of use of IMGT website. (see http://www.imgt.org/ for details). -n Press ENTER to continue or other key to exit...

./importFromIMGT.sh: line 40: syntax error near unexpected token (' ./importFromIMGT.sh: line 40:done < ($wg 'http://imgt.org/genedb/' | pup '#Species option attr{value}' | grep -v any )'

[dbolotin]

Thanks for reporting!

Strange error, I checked on 10.11.5, and as I remember it also worked on 10.11.4 .

Could you please confirm that line 40 of your copy of the script contains two < symbols, like in original file:

done < <($wg 'http://imgt.org/genedb/' | pup '#Species option attr{value}' | grep -v any )

[marcovth]

On 2016-05-30 5:23 PM, Dmitry Bolotin wrote:

Thanks for reporting!

Strange error, I checked on 10.11.5, and as I remember it also worked on 10.11.4 .

Could you please confirm that line |40| of your copy of the script contains two |<| symbols, like in original file https://github.com/milaboratory/mixcr/blob/master/importFromIMGT.sh#L40:

done < <($wg 'http://imgt.org/genedb/' | pup '#Species option attr{value}' | grep -v any )

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Hello ...

Here is a screenshot from a brand new MacPro, but the unaltered, original, script gave the exact same error with an older MacPro ...

I rebooted the new MacPro to make sure the newly installed brew tools were active, and it gave the same error.

Hope this helps.

Thanks for the service.

• Marco.

[dbolotin]

Could you please submit screenshot using GitHub interface, as it didn't attache properly last time.

Please, provide some instructions on how to reproduce the problem. I checked the script with both built-in bash and with bash 4.3 installed using brew, and everything works perfectly. I am on 10.11.5, but I don't think something changed from 10.11.4, or even from Mountain Lion... What shell are you using? Script also works on at least 4 Mac's in our lab.

Try to run script through mixcr script:

./mixcr importFromIMGT

[marcovth]

Your last commend solved the issue. I ran the script with sh ./importFromIMGT.sh instead of mixcr importFromIMGT.

Thanks.

[dbolotin]

Good! I'll remove notion about direct execution of the script from docs.