Question: Galaxy Url for Fasta and Bed index files
0
gravatar for asmariyaz23
22 months ago by
asmariyaz2310
United States
asmariyaz2310 wrote:

Hello,

What is an appropriate galaxy URL to use to obtain bed and fasta index files? I have tried below:

myGalaxy.org:port/dataset/get_metadata_file?hda_id=[fasta_dataset_id]&metadata_name=fasta.fai {for fasta index}

and 

myGalaxy.org:port/dataset/get_metadata_file?hda_id=[bed_dataset_id]&metadata_name=bed.idx {for bed index}

While looking through metadata for both bed and fasta file at:

myGalaxy.org:port/api/histories/[history_id]/contents/[api_id]

I realized that it lacks a meta_files list which is unlike the case with bam files which is filled with bam_index. Is there a way to populate this list for bed and fasta files as well?

Thank you

Asma

 

 

fasta bed galaxy index • 450 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by asmariyaz2310
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello, Are you generating these index files yourself? If so, how? What exactly do they represent? BAM index files are an inherent part of the data type. This is not true for bed and fasta datatypes (and most others).

If the question is instead how to access metadata for datasets via the API, then that is different content.

Thanks! Jen, Galaxy team

 

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson22k
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