Framework for submitting proteomics data to the PRIDE archive at EBI
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Register with PRIDE website at 'https://www.ebi.ac.uk/pride/archive/'.
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Contact '[email protected]' to obtain your FTP credentials.
Visit 'http://www.ebi.ac.uk/pride/help/archive/submission' to get more information about submitting data to PRIDE.
The following system dependencies are required to be installed BEFORE anadama-pride can be installed and executed:
- Python 2.7
- Java x86_64 (1.8 or higher)
- Git
- Python Setuptools
- Python Pip
- Aspera ascp client
On a Debian or Ubuntu system, the following command will install these and whatever secondary dependencies they may have:
$ sudo apt-get install python2.7 python-pip python-setuptools git openjdk-8-jre-headless
- Obtain the anadama-pride requirements.txt file
The anadama-pride tool has its own set of Python requirements, which are captured in a requirements.txt file that lists the python libraries as dependencies.
$ curl -O https://raw.githubusercontent.com/ihmpdcc/anadama-pride/master/requirements.txt
This will download the requirements.txt file and place it into your current working directory.
- Install the software
Using the 'pip' utility, one can easily install all the dependencies with a simple command, like so:
$ pip install -r requirements.txt
Pip will install the various tools, libraries, and scripts, including anadama-pride. When complete, you should see "cutlass", "osdf-python", "anadama", and "pride" when you execute the following command:
$ pip list
- Update the configuration file ‘.anadama_pride’.
A skeletal configuration file is included with the installation of anadama-pride and is located in the directory containing the pride python module. Users have the option of editing this file directly (if they have the necessary O/S permissions), or they can create an .anadama_pride file in their home directories. Another possible location is in the default python search path, or any directories enumerated in the PYTHONPATH environment variable. While searching for the configuration file, anadama-pride searches for the .anadama_pride configuration file in the following locations, in order:
- Home directory
- Source code directory
- Python path (and PYTHONPATH locations)
The .anadama_pride configuration file is in the following format, and needs values to be appended to each setting:
dcc_user=
dcc_pw=
pride_user=
pride_pw=
pride_server=
pride_directory=
submitter_name=
submitter_email=
submitter_affiliation=
lab_head_name=
lab_head_email=
lab_head_affiliation=
submitter_pride_login=
project_title=
project_description=
If any of the above settings are left blank (unconfigured), anadama-pride will error out wih the following message:
Please update the configuration file with the required metadata.
- Running the pipeline command:
Users can invoke the pipeline in two ways:
- Using the basic pipeline command and providing the OSDF id of the study to be submitted interactively when prompted.
anadama pipeline run
- Passing the OSDF id of the study to be submitted as a command line argument when starting the pipeline.
anadama pipeline pride -o ‘collect.study_id:<study-id>’
- Help
Additional help information can be read by the following commnads
anadama help pipeline pride
anadama help pipeline
anadama help
Email PRIDE support at '[email protected]' to notify them about your submission or inquire into the status of the submission.