Hi @Shaadi_Mehr
You should be able to load a genome fasta and sequence fastq files directly into Galaxy from NCBI. (same for the reference annotation gtf)
This is a recent post where I loaded up reference data →
Another example with a different species →
- Inquiry about lettuce genome plus any posts with a custom-genome tag.
Then, for fastq data there are dedicated tools. These retrieve using accession IDs. The tutorial covers how to source the accession IDs but if you already have them you can skip down to the tool where just the list of accessions is given.
I’m not sure about that service. The Galaxy requirement is that a link is “public” and anyone can access the file directly without credentials or passwords in the URL string.
If the link is instead just a pointer to a file, this is usually where the problems come up with trying to resolve it through too many redirects/cookies on the hosting site. I suspect this site applies a lot of tracking and might be a problem, but you could try it to see what happens.
You should be able to load 2 GB of fastq data without any problems.
If you are having a problem – try loading using all defaults. You will want Galaxy to “guess” the datatype format. I can help with this if you share an example.
In some extreme cases, uncompressing before loading is needed (a much older version of gzip or similar). But this should be really rare.
So, in short:
- Load public data directly from the data provider whenever possible
- Upload local data using all defaults
- Run some sanity checks once the content is in Galaxy. This is usually just a few cleanup steps to simplify the formats.
Hope this helps and we can follow up more!