Question: running samtools faidx
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jannetta.steyn • 10 wrote:
Is it possible to run samtools faidx in Galaxy? If so how?
Thanks for any help Jannetta
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Jennifer Hillman Jackson ♦ 25k wrote:
Hello,
Creating sam indexes for database (genome, transcriptome, etc) is possible on a local or cloud Galaxy by installing and using this Data manager:
Import and index the database first with one of these Data Managers:
- Use when the database is already in the builds list: data_manager_fetch_genome_all_fasta
- Use when adding a new database to the builds list: data_manager_fetch_genome_dbkeys_all_fasta
The "builds list" is the list of databases that can be found in the upload tool's list of databases, or by clicking on the pencil icon for any dataset to reach the Edit attributes page's list of builds/databases, or in the Admin section under Local Data -> Data Managers -> Tables (lower section) "all_fasta.loc"
Hopefully this helps, Jen, Galaxy team
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jannetta.steyn • 10 wrote:
So is it not possible on usegalaxy.org?
No, genomes are indexed for tools by the administrators of the instance.
If the genome you wish to use is not included on an instance, it can be used as a custom genome (and build, assigned to the dataset prior to using Sam/Picard tools). More here: https://wiki.galaxyproject.org/Support#Custom_reference_genome
Requests for genomes are also accepted for consideration. These should be public datasets available at NCBI. Current list of new indexes in progress and where to make the request: https://github.com/galaxyproject/galaxy/issues/1470
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