On Tue, Apr 22, 2014 at 4:34 PM, Ulf Schaefer <ulf.schae...@phe.gov.uk> wrote:
> Hi Peter
>
> I removed the unnecessary code.
>
> If I run the tool with just a couple of inputs I see entries in the log
> files either from galaxy.jobs.runners.drmaa or from
> galaxy.jobs.runners.local that the job is being dispatched as normal.
>
> Unfortunately there is no sign of the job in the log files when using
> more input files.
>
> The command line that is supposed to be run is:
>
> bash home/galaxy/galaxy-dist/tools/vcf_processing/vcf_to_fasta.sh
> /galaxy/database/files/042/dataset_42275.dat 40 10 50 0 40 0.9 20
> /galaxy/database/files/041/dataset_41720.dat,
> /galaxy/database/files/041/dataset_41980.dat,
>
> the first dat file being the output and the ones at the end being a
> comma separated list of the input files. On the command line this
> command works with much longer input files lists.

I wouldn't bother with the commas - that is just wasting characters
and eating into the maximum command line string length.

> Any ideas?

Check the limit with "xargs --show-limits" or "getconf ARG_MAX",
our CentOS server reports:

$ getconf ARG_MAX
2621440

> Or is there a better practice to pass a large number of input
> files to a bash script?
>
> Thanks
> Ulf

If there is any chance of your constructed command line string
exceeding the system limit, I would construct an input file
containing the filenames (e.g. one per line). That might be
a practical solution anyway.

For the file bases approach, I would used the Galaxy <configfile>
tag. Some of the tools bundled with Galaxy also use this (find
them with grep), or for example one of mine:

https://github.com/peterjc/pico_galaxy/blob/master/tools/mira4/mira4_de_novo.xml

Regards,

Peter
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