galaxy-upload

galaxy-upload is used to upload bigwig and bed files to usegalaxy.org and to generate links to view those files in UCSC genome browser.

Prerequisites

If using Docker, the only prerequisite is to install docker CE.

If using outside of Docker, the requirements can be installed using

conda install -c bioconda --yes --file requirements.txt

Building

docker image build -t galaxy-upload .

Running

galaxy-upload can be run with and without Docker, though the latter is recommended.

Running galaxy-upload requires an account at usegalaxy.org.

The API key for your galaxy account can be obtained from User->Preferences->Manage API key.

Without Docker:

upload.py username api_key dir proj_name

  username    Username for usegalaxy.org.
  api_key     API key obtained from usegalaxy.org.
  dir         Directory of bigWig and junctions.bed files to upload.
  proj_name   Name to give track file. Existing track files with same name
              will be overwritten.

  Generated links can be found in {proj_name}_URL.txt in the same directory.

With Docker:

TODO