Re: [galaxy-dev] using DataManager to add custom genomes
Hi Nikhil, Have a look at https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta to add a new genome/fasta. Once you have the genome entry, then you can use additional Data Manager to make tool specific (bwa, samtools, etc) indexes. Thanks for using Galaxy, Dan On Apr 2, 2015, at 5:41 AM, Nikhil Joshi wrote: > Of course this would be for a local install of galaxy. > > On Thu, Apr 2, 2015 at 2:29 AM, Nikhil Joshi wrote: > Hi all, > > Is it possible to use a DataManager (or anything) to allow a user (or admin) > to upload their genome of choice and have it be indexed and be used as a > built-in/cached genome *without* having to go on the command-line? I.e., only > using the Galaxy interface? > > - Nik. > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > najoshi -at- ucdavis -dot- edu > 530.752.2698 (w) > > > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > najoshi -at- ucdavis -dot- edu > 530.752.2698 (w) > ___ > 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/
Re: [galaxy-dev] using DataManager to add custom genomes
Of course this would be for a local install of galaxy. On Thu, Apr 2, 2015 at 2:29 AM, Nikhil Joshi wrote: > Hi all, > > Is it possible to use a DataManager (or anything) to allow a user (or > admin) to upload their genome of choice and have it be indexed and be used > as a built-in/cached genome *without* having to go on the command-line? > I.e., only using the Galaxy interface? > > - Nik. > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > najoshi -at- ucdavis -dot- edu > 530.752.2698 (w) > -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] using DataManager to add custom genomes
Hi all, Is it possible to use a DataManager (or anything) to allow a user (or admin) to upload their genome of choice and have it be indexed and be used as a built-in/cached genome *without* having to go on the command-line? I.e., only using the Galaxy interface? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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/
