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: [email protected] 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 <[email protected]> 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/
