Hi Jochen,

Don't have it use /tmp, but rather the current working directory and
then everything will work. Galaxy jobs are run in individual working
directories, so you can exploit that to ensure that files aren't
overwritten.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, Jan 4, 2017 at 12:32 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
> Hi,
>
> I have a tool that produces multiple output files a log file, two bam files.
> (https://github.com/nugentechnologies/nudup)
>
> The tool it self provides an option called --out to specify a path to a
> directory with a prefix that will be added to the output files:
>
> --out /tmp/out
>
> this will produce 3 files:
>
> /tmp/out_dup_log.txt
> /tmp/out.sorted.dedup.bam
> /tmp/out.sorted.markdup.bam
>
> so my question is if this out prefix will give me problems overwriting next
> output files coming from this tool?
>
>
> Cheers Jochen
>
>
>
> ___________________________________________________________
> 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:
>  https://lists.galaxyproject.org/
>
> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to