COG-UK Docs

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Updated 2020-10-02 by @samstudio8

Uploading library and run metadata with Ocarina

In the case where a sample has been transferred from one site to another to be sequenced, the sequencing site should not need to upload any biosample metadata. This document describes how to upload library and sequencing metadata with Ocarina on the command line. If you want to use the web-based metadata uploader to do this, see the documentation here.

Notes

Uploading metadata with Ocarina

0. Install Ocarina

Run the following command in your shell. You should be running python 3.7 and have pip installed. Feel free to do this from a virtualenv or conda environment.

pip install git+https://github.com/samstudio8/ocarina.git

This will install the latest development version of Ocarina, which almost always works.

1. Configure Ocarina

See the Ocarina README for configuration instructions. You will need your API key from your Majora profile.

2. Register a library

This ocarina command will register a sequencing library. You will need to replace the options with the relevant information.

ocarina put library --library-name "BIRM-20200326-1844" \
                --library-seq-kit "LSK109" \
                --library-seq-protocol "LIGATION" \
                --library-layout-config "SINGLE" \
                --biosamples HOOT-OCARINA-101 HOOT-OCARINA-102 \
                --apply-all-library VIRAL_RNA PCR AMPLICON MYPROTOCOL MYPRIMERS

3. Register a sequencing run

This ocarina command will register a sequencing run. You will need to replace the options with the relevant information.

ocarina put sequencing --library-name BIRM-20200326-1844 \
                   --run-name "20200409-1840_MYRUN_000000_FAK12345" \
                   --instrument-make "OXFORD_NANOPORE" \
                   --instrument-model "GRIDION"

Troubleshooting


Published 2020-09-28. Updated 2020-10-02. Page maintainer @samstudio8.