My goal is to use a JSON file (which is a product of a lab implemented pipeline ran on galaxy) for visualizing 2 BAM files (also produced by the pipeline) loaded in history.
For this purpose I started out by loading the BAM and JSON individually in history and working my way from there (as I haven't looked into generating API IDs and history ID dynamically through scripts).
I load a BAM file in history, extract it's history ID and API ID (which I later use in my JSON file to indicate where galaxy should find the file). Here is a small part of what the JSON file looks like:
{
"CLL-HL_pilot.r1.fastq": {
"DNA": "/api/histories/a799d38679e985db/contents/3f5830403180d620/display",
"DNA_INDEX": "test.dna.bai",
"DNA_VCF": "test_DNA.vcf",
"FN": {
"Chr1-144915561 (203)": {
"Alt": "G",
"Chr": "1",
"Cov": "227",
"Cov_dna": "203",
"Loc": "144915561",
"Ref": "NA",
"Strand": "+"
},
I want to use this JSON file to pass information into a JS which creates the IGV tracks and loads the BAM file. I keep ending up with a file not found error.
http://kcodevel.broadinstitute.org:8088/galaxy/visualization/show/api/histories/a799d38679e985db/contents/3f5830403180d620/display (404) NOT FOUND.
When I go to the link above the actual BAM file gets downloaded so I know that the correct URL is being used, I just can't figure out how to provide a valid URL/path to the BAM file in history.
Note: I already have JSON data provider and visualization created in my local instance in galaxy which is configured with apache. Another test made was to try doing the same thing but without apache in place but I end up in the same problem.
Appreciate any help I can get!
Asma
