Don't have a ton to add to Peter's suggestion I just wanted chime in that there is definitely not some inherit Galaxy limit on the backend for the number selections allow in a multiple input widget. I just tried a test with 4 times this number of inputs and it worked fine. This could well be reaching some sort of maximum command line length - but 20 some files seems a very low limit - in the past when I have hit such limits it has been on hundreds or thousands of files - not dozens.
It is difficult to work with a large number of inputs because select2 takes over in the UI and provides a very frustrating data input experience for these inputs (see conversation here http://dev.list.galaxyproject.org/HTML-form-of-select-parameter-tt4663142.html). It may be worth applying this patch (https://bitbucket.org/galaxy/galaxy-central/pull-request/379/disable-select2-for-all-multi-select/diff) suggested by Jeremy in that thread to simplify the tool UX and try again. -John On Tue, Apr 22, 2014 at 11:23 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/