This is a set of scripts to that utilize bioblend to interact with the Galaxy API.
Python 2.7
Bioblend 0.11.0
After cloning edit these files:
- util/config.py.template ( copy it to util/config.py and add server and port to the dictionary)
on your .bashrc add the line
export API_KEY=
Where the API_KEY is the Admin Galaxy API key created from the GUI
before using any script you must source the python env
source /cvmfs/soft.galaxy/v2/server/.venv/bin/activate
This Galaxy option must be set to a dir inside galaxy server.
library_import_dir = /srv/galaxy/galaxy-data-library/
Before using this script create a yaml file following the template yml_file/library.yml.
This script creates a Galaxy Library from one of three different sources: local file, url or from remote server (symlink).
- Local will upload files from your machine to the Galaxy Library
- Url will fetch the files from a remote server and upload to the Galaxy Library
- Server will take file aready in the Galaxy server and symlink them to the Galaxy Library.
The script will know which option (local, url, server) to use based on the yaml file.
python create_library.py yaml_file.yml
This script creates a pickled version of the Galaxy library, where the file name is the key and the Galaxy file id is the value. This speed up the lookup for file IDs.
This script must be run after the Library creation and at every new library release.
python pickle_library_dataset.py -l library_name [optional -d path to the pickled file will be created]
The script help
usage: pickle_library_dataset.py [-h] -l LIBRARY [-d DUMP]
A tool to create binary dictionary of a Galaxy library where the keys are file
namesand the values are file ids
optional arguments:
-h, --help show this help message and exit
-l LIBRARY, --library LIBRARY
Name of the library holding the files.
-d DUMP, --dump DUMP A path to the directory where de library will be
dumped. Default lib_dump
This Galaxy option must be set to True. The Galaxy authetication must be handled by a proxy. If not the option -email of the script will be required and the script will not create random accounts.
use_remote_user = True
This script creates a user on Galaxy (if it does not exists), handles its authentication, and adds to the user's history all datasets passed to it (inside of a file). The datasets must be inside of the Galaxy Library. Use the create_libary.py to create the library before
The script can also delete users from Galaxy.
# Create a random user and add datasets from IHEC library to a new history
python transferDataSetIhec.py -l IHEC -s dataset-list.txt
#Connect to a specific user account and add datasets from IHEC library to a new history
python transferDataSetIhec.py -l IHEC -s dataset-list.txt -e [email protected]
#Connect to a specific user account and add datasets from IHEC library to a existing history
python transferDataSetIhec.py -l IHEC -s dataset-list.txt -e [email protected] -his 87hg7gg6g6gf
NOTE: pass the --dump argument if the pickled library is not at its default location (lib_dump)
The dataset-list.txt file is a file containing the path of each dataset that will be imported in the user's history. This path must reflect the path inside of the Galaxy Library.
if for example a Library called IHEC contain this path
IHEC/consortia/species/file1.bigwig
IHEC/consortia/species/file2.bed
The dataset-list.txt should be
/consortia/species/file1.bigwig
/consortia/species/file2.bed
The script help
A tool to create user on Galaxy and transfer IHEC datasets to the user history
optional arguments:
-h, --help show this help message and exit
-s SAMPLES, --samples SAMPLES
File with the sample's Libary path
-d DELETE, --delete DELETE
Id of the user to be deleted
-e EMAIL, --email EMAIL
User email on Galaxy (if user is already registered)
-his HISTORY_ID, --history_id HISTORY_ID
A Galaxy history id. If provided the files will be
uploaded to this history.
-l LIBRARY, --library LIBRARY
Name of the library holding the files.
--dump DUMP A path to the directory where de library dictonary was
dumped. Default lib_dump