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.
central_sample_id that was provided to you
Run the following command in your shell. You should be running python 3.7 and have
Feel free to do this from a
pip install git+https://github.com/climb-covid/ocarina2.git
This will install the latest development version of Ocarina, which almost always works.
See the Ocarina README for configuration instructions. You will need your API key from your Majora profile.
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
library-name is the name of the library pool, it needs to be unique and is only used to map sequencing runs to libraries
library-seq-kit is the kit used for the library pooling
library-seq-protocol is the protocol used for the library pooling
library-layout-config should be
biosamples is a list of
central_sample_id (COGIDs) that were pooled onto this sequencing library
apply-all-library is an ordered set of properties applied to all samples, they must be filled in the following order:
SOURCE (e.g. VIRAL_RNA)
SELECTION (e.g. PCR)
STRATEGY (e.g. AMPLICON)
PROTOCOL the protocol you are using (e.g.
PRIMERS if you’re using the ARTIC primer scheme, just enter the version number (e.g.
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" \
library-name is the name of the library pool that you registered in the previous step (you must have registered the library first)
run-name is the name of the sequencing run, as named by your sequencer
instrument-make should be
instrument-model is the model of your sequencer (e.g.
ocarina reports a
STATUS CODE 400, you have not authenticated correctly. Check the API key in your config file (
~/.ocarina) has not expired.
At least one Biosample in your Library was not registered. No samples have been added to this Library. Register the missing samples, or remove them from your request and try again, it indicates that your barcode is missing from Majora. If the sample originated from WSI it is guaranteed they will exist, so this error indicates a barcode has been entered incorrectly in your request.
apply-all-library parameter matters, any deviation from this will cause an error.