Test atlas

If you want to test atlas on a small example data here is a two sample, three genome minimal metagenome dataset, to test atlas. Even when atlas will run faster on the test data, it will anyway download all the databases and requirements, for the a complete run, which can take a certain amount of time and especially disk space (>100Gb).

The database dir of the test run should be the same as for the later atlas executions.

The example data can be downloaded as following:

git clone https://github.com/metagenome-atlas/example_data.git

We initialize a atlas working directory testrun using the test reads. The reads are paired end stored in one file therefore we set the --interleaved-fastq flag. The test samples don’t require a lot of threads (set to 2), they do require However some memory (~60GB).:

atlas init --db-dir databases --working-dir testrun --interleaved-fastq --threads=2 example_data/reads/test

After the set up you can run:

atlas run --working-dir testrun

Test atlas using docker container

Testing atlas using the docker container works similarly to the above example.

Create a working directory:

mkdir DockerTest; cd DockerTest

get the example data:

git clone https://github.com/metagenome-atlas/example_data.git

Set up the docker as explained here and run it:

mkdir -p AtlasDB/GTDB-TK AtlasDB/EggNOGV2
docker run -i -u $(id -u):$(id -g) -v $(pwd):/WD -v $(pwd)/AtlasDB/EggNOGV2/:/databases/EggNOGV2 -v $(pwd)/AtlasDB/GTDB-TK/:/databases/GTDB-TK -t metagenomeatlas/atlas:latest /bin/bash

Inside the docker you have access to the example_data and you can initialize and run atlas test example as above.