Hello Galaxy-dev,
I thank you so much for all the help you have given me.
I have a question about data set ids in galaxy. As a background, I am running my own galaxy instance on a server. A pipeline implemented in the lab produces the following files in the history:
1) 2 BAM files 2) A JSON file
My goal is to use this JSON file to pass the path/URL of bam files into a custom JS we wrote for visualization purpose.
This JSON file contains among many other details the paths/URLs to the above bam files. I am using JSON filetypes to send data to the JS visualization within Galaxy. To do this, I have my own JS which loads a BAM file from URL provided into an IGV.js track. IGV.js, which is responsible for making the tracks, expects a valid URL which is updated in the JSON file in this manner:
1) Extract the API_key and history id from a loaded BAM file 2) Edit the JSON file to reflect the BAM file's dataset id to be something like this:
{ "CLL-HL_pilot.r1.fastq": { "DNA": "/datasets/36ddb788a0f14eb3/display?to_ext=bam", ...
This works fine if I know the API Key for bam files. When a pipeline executes dataset ids are generated for each output. I want to access and include these ids in the JSON file and load the updated JSON file into the history with the bams. Is there a way to get the ids from the history in this manner?
Thank you,
Asma