Meteor is INRAE MetaGenoPolis internal pipeline.
Docker Source: https://github.com/gmtsciencedev/bioit-dockers
Meteor sources: https://forgemia.inra.fr/metagenopolis/meteor
In this example we will use the IGC2 catalog with meteor.
First, you will need the IGC2.fna.gz file here: https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.15454/FLANUP
This small python script will reindex the catalog, creating the IGC2_reindexed.fa catalog that we will use.
import gzip
with gzip.open('IGC2.fna.gz','rt',encoding='utf-8') as source:
with open('IGC2_reindexed.fa','w', encoding='utf-8') as reindexed:
with open('IGC2_index.tsv','w', encoding='utf-8') as index:
index.write('number\tannotation\n')
n = 1
for line in source.readlines():
if line.startswith('>'):
name=line[1:].strip()
reindexed.write(f'>{n}\n')
index.write(f'{n}\t{name}\n')
n += 1
else:
reindexed.write(line)
Place the IGC2_reindexed.fa file in a folder, lets say /resource.
Next build the index with:
docker run --rm -it -v /resource:/resource gmtscience/meteor MeteorReferenceBuilder.rb -i IGC2_reindexed.fa -1 -p /resource -n IGC2
You will need around 30GB of memory for this building step.
Content type
Image
Digest
sha256:13e26a296…
Size
474.1 MB
Last updated
over 3 years ago
docker pull gmtscience/meteor