I wanted to upload mu trimmed reads to galaxy and map them using bowtie, but the only task I was able to complete was uploading my file from computer. When uploading is done the status of uploading job (and every new job I'm trying to start - fastq groomer, bowtie, uploading reads from url) is "job is waiting to run". What should I do?
On our public server, the only option (currently) for that situation is to wait for the jobs to run. This happens periodically when the server is under heavy use.
Another option if you need immediate access would be to use your own cloud instance. See https://wiki.galaxyproject.org/Cloud for details.