The Rfam Batch Search can be used to submit a sequence to the Job Dispatcher service that runs the Infernal cmscan software
- Clone Git repository:
git clone https://github.com/Rfam/rfam-batch-search.git
- Run Docker Compose:
docker-compose up --build
To run unit tests, use
docker exec rfam-batch-search_web_1 pytest ./tests/test_api_file.py
Requirements
# Make sure you are using the correct namespace
% kubectl config current-context
rfam
# List helm charts
% helm list --all
NAME NAMESPACE REVISION UPDATED STATUS CHART APP VERSION
batch-search rfam 1 2024-05-10 11:04:58.920023 +0100 BST deployed helm-0.1.0 1.16.0
# Uninstall chart
% helm uninstall batch-search
release "batch-search" uninstalled
# Install chart. It is possible to set some variables here,
# but the main one is the branch.
% cd kubernetes/helm
% helm install batch-search . --set branch=dev
NAME: batch-search
LAST DEPLOYED: Fri May 10 11:04:58 2024
NAMESPACE: rfam
STATUS: deployed
REVISION: 1
TEST SUITE: None
# Follow the pods creation by running the command below
% kubectl get pod
NAME READY STATUS RESTARTS AGE
nginx-5dbfc595db-dndt2 1/1 Running 0 3s
nginx-5dbfc595db-smhwm 1/1 Running 0 3s
rfam-batch-search-59657595ff-6lrhp 0/1 ContainerCreating 0 3s
rfam-batch-search-59657595ff-qdgjp 0/1 ContainerCreating 0 3s
rfam-batch-search-59657595ff-t4vs7 0/1 ContainerCreating 0 3s
rfam-batch-search-59657595ff-t8m5p 0/1 ContainerCreating 0 3s