Mytax2 - Realtime reporting

Create Conda Environment

conda env create -f environment.yml

Project setup

npm install

Starting Development

Run the below 2 commands:

Compiles and hot-reloads for development on frontent

npm run serve

Compiles and hot-reloads for development on server

npm run server

Building Production package

npm run build

Lints and fixes files (development only)

npm run lint

Customize configuration

See Configuration Reference.

Samplesheet input

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. By default, it will always look in the /data/Samplesheet.csv file for your desired deployment method. For example, in dev mode it will be public/data/Samplesheet.csv, for production (like in a Docker container running nginx like what is described below) it is in <path_to_dist>/data/Samplesheet.csv. If you want to check if it is accesible, you can access it at the localhost and port with the path like localhost:8080/data/Samplesheet.csv (this is the default dev port)

The Samplesheet should look like (example below) this

sample,path_1,path_2,format,platform,database,compressed
NB11,<path_to_directory>/NB11,,directory,oxford,<path_to_database_directory>/flukraken2,
NB03,<path_to_directory>/NB03,,directory,oxford,<path_to_database_directory>/flukraken2,
ERR6913101,<path_to_directory>/ERR6913101_1.fastq.gz,<path_to_directory>/ERR6913101_2.fastq.gz,file,illumina,<path_to_database_directory>/flukraken2,
ERR6913102,<path_to_directory>/ERR6913102_1.fastq.gz,<path_to_directory>/ERR6913102_2.fastq.gz,file,illumina,<path_to_database_directory>/flukraken2,
flu_bc01,<path_to_directory>/flu_BC01.fastq,,file,oxford,<path_to_database_directory>/flukraken2,
sample,<path_to_directory>/sample_metagenome.fastq,,file,oxford,<path_to_database_directory>/flukraken2,
test,test2.fastq,,file,illumina,<path_to_database_directory>/flukraken2,

Column	Description
`sample`	Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`).
`path_1`	Full path to FastQ file for Illumina short reads 1 OR OXFORD reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".
`path_2`	Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".
`format`	TRUE/FALSE, is the row attributed to a demultiplexed barcode folder of 1 or more fastq files or is it a single file that is .gz?
`platform`	Platform used, [ILLUMINA, OXFORD]
`compressed`	TRUE/FALSE, is your set of files compressed or not as `.gz` format column
`pattern`	Pattern to match items (regex) for barcoded runs
`kits`	List of guppy barcode kits for barcode runs. Such as `EXP-NBD103` and `SQK-LWB001`

An example samplesheet has been provided with the pipeline alongside some demo data.

Creating a Docker image using the pre-built code.

conda activate mytax2

npm run build;

docker build . -t jhuaplbio/basestack_mytax2;

This will first activate the necessary conda env mytax2. Then, it will build the compressed and compiled production app. Finally, it will make the Docker image and copy the bundled files into the image for use

Get minikraken2 database

mkdir -p data/databases
wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz -O ./data/databases/minikraken2.tar.gz 
tar -xvzf ./data/databases/minikraken2.tar.gz && rm -rf data/databases/minikraken2.tar.gz
mv minikraken2_v2_8GB_201904_UPDATE data/databases/

Running a container with the nginx service at port 8098 on localhost

docker container run -it --rm -p 8098:80 jhuaplbio/basestack_mytax2  bash -c "nginx; bash "

License and copyright

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.

jhuapl-bio/mytax