Sage-Bionetworks/synapse-seq

Name: synapse-seq

Owner: Sage Bionetworks

Description: Code for running/loading seq datasets using Synapse.

Created: 2013-12-04 22:57:18.0

Updated: 2016-07-29 23:21:29.0

Pushed: 2016-08-26 00:26:31.0

Homepage: null

Size: 98

Language: Python

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README

synapseseq

This package contains functionality to load existing seq datasets into Synapse and to run seq workflows using Synapse.

This software is in early alpha stage – please contact the author before attempting to use.

Installing

Clone the git repo, or download the zip, or to install local git repo:

sudo pip install -e /path/to/local/repo

Dependencies

synapse python client, qsub

Usage

Running seq workflows using synapse

Quick overview:

1. Install synapse python client and synapseseq.
2. Using synapse client, create evaluations for all workflow components you want to use (components are found in scripts/).
3. Edit the file eval-code-assignment.yaml to include the ids for the evals you created in step #2. Upload the file to synapse and edit scripts/eval_listener to point to this entity.
4. Setup scripts/eval_listener.py to run on a cron job or other comparable method.
5. Upload input files to synapse or external AWS S3 bucket and submit them to desired seq workflows (aka evals). Outputs will be loaded to synapse with provenance and annotations.

Compute requirements:

Currently, qsub is used to manage all jobs across the compute resource. Other job management software may be added in the future.

Loading existing datasets into Synapse.

Will add this text in near future.

License and Copyright

© Copyright 2013 Sage Bionetworks

This software is licensed under the Apache License, Version 2.0.