Re: [galaxy-dev] Tool Development DELLY
Hi Marco, No problem - I originally copied the metadata access trick from one of the Galaxy dev-team's tool anyway. Maybe we need to add this to the wiki... Peter On Tuesday, January 13, 2015, Marco Albuquerque < marcoalbuquerque@gmail.com> wrote: > Hi Peter, > > I was unaware of how to access metadata, that seemed to be my issue. The > tool works now though! > > Thanks so much, > > Marco > > > > > On 2015-01-09 7:13 PM, "Peter Cock" > wrote: > > > >I think the symlink approach is best, see for example the Python > >wrapper script I used here for "samtools idxstats", > > > https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats > > > >However, you can make the link in the XML directly, see Dave's > >reworking of this wrapper: > > > https://github.com/galaxyproject/tools-devteam/tree/master/tool_collection > >s/samtools/samtools_idxstats > > > >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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Development DELLY
On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque wrote: > Hello Galaxy, > > I'm currently working on adding some tools and am having an issue with > DELLY. > > So, I am under the impression that BAM indexing happens automatically when a > BAM is uploaded. However there is no associated dataset_i.dat.bai file in > the file location in my local instance of galaxy. > > There is however metadata which seems to be created but they are not being > linked together. What I mean to say is DELLY errors with cannot find Bam > Index. > > I was curious if there is a specific way developers are suppose to work > around this? Basically we want to avoid having to provide both the BAM and > BAM index and symbolically linking a new dataset because we know you have > already created a better implementation, we just want to use it and don't > know how. > > Any help is greatly appreciated, > > Marco I think the symlink approach is best, see for example the Python wrapper script I used here for "samtools idxstats", https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats However, you can make the link in the XML directly, see Dave's reworking of this wrapper: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool Development DELLY
Hello Galaxy, I'm currently working on adding some tools and am having an issue with DELLY. So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy. There is however metadata which seems to be created but they are not being linked together. What I mean to say is DELLY errors with cannot find Bam Index. I was curious if there is a specific way developers are suppose to work around this? Basically we want to avoid having to provide both the BAM and BAM index and symbolically linking a new dataset because we know you have already created a better implementation, we just want to use it and don't know how. Any help is greatly appreciated, Marco ___ 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/
