GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → soedinglab → MMseqs2-App

soedinglab / MMseqs2-App

Licence: GPL-3.0 License
MMseqs2 app to run on your workstation or servers

Programming Languages

javascript
184084 projects - #8 most used programming language
go
31211 projects - #10 most used programming language
Vue
7211 projects
CSS
56736 projects
Makefile
30231 projects
shell
77523 projects

Labels

electrondockerbioinformaticsvuedocker-composeprofile-searchsequence-searchmmseqs

Projects that are alternatives of or similar to MMseqs2-App

SemiBin
No description or website provided.
Stars: ✭ 25 (+56.25%)
Mutual labels:  bioinformatics
RNAseq titration results
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Stars: ✭ 22 (+37.5%)
Mutual labels:  bioinformatics
docker-compose-v3
No description or website provided.
Stars: ✭ 15 (-6.25%)
Mutual labels:  docker-compose
PCG
𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
Stars: ✭ 20 (+25%)
Mutual labels:  bioinformatics
antigen.garnish
No description or website provided.
Stars: ✭ 34 (+112.5%)
Mutual labels:  bioinformatics
bacnet
BACNET is a Java based platform to develop website for multi-omics analysis
Stars: ✭ 12 (-25%)
Mutual labels:  bioinformatics
snpsea
📊 Identify cell types and pathways affected by genetic risk loci.
Stars: ✭ 26 (+62.5%)
Mutual labels:  bioinformatics
PhyloTrees.jl
Phylogenetic trees in Julia
Stars: ✭ 15 (-6.25%)
Mutual labels:  bioinformatics
docker4ruby
Docker-based Ruby stack (works for Rails)
Stars: ✭ 27 (+68.75%)
Mutual labels:  docker-compose
mongodb-replica-set
Docker setting for mongodb replica set
Stars: ✭ 21 (+31.25%)
Mutual labels:  docker-compose
conda-env-builder
Build and maintain multiple custom conda environments all in once place.
Stars: ✭ 18 (+12.5%)
Mutual labels:  bioinformatics
genomedisco
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
Stars: ✭ 23 (+43.75%)
Mutual labels:  bioinformatics
fermikit
De novo assembly based variant calling pipeline for Illumina short reads
Stars: ✭ 98 (+512.5%)
Mutual labels:  bioinformatics
EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
Stars: ✭ 25 (+56.25%)
Mutual labels:  bioinformatics
GenomeAnalysisModule
Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
Stars: ✭ 19 (+18.75%)
Mutual labels:  bioinformatics
dna-traits
A fast 23andMe genome text file parser, now superseded by arv
Stars: ✭ 64 (+300%)
Mutual labels:  bioinformatics
cv4pve-metrics
Metrics for Proxmox VE, Grafana with dasboard, InfluxDb
Stars: ✭ 38 (+137.5%)
Mutual labels:  docker-compose
docker-parse-mongo
Parse Server with MongoDB ReplicaSet using Docker (for AWS EC2 or GCP GCE)
Stars: ✭ 27 (+68.75%)
Mutual labels:  docker-compose
obi
The Ontology for Biomedical Investigations
Stars: ✭ 49 (+206.25%)
Mutual labels:  bioinformatics
micca
micca - MICrobial Community Analysis
Stars: ✭ 19 (+18.75%)
Mutual labels:  bioinformatics
View All Similar Projects ➔

MMseqs2 App and Server

MMseqs2 is a software suite to search and annotate huge sequence sets. We built a graphical interface to make it more useful for interactive data exploration. Check out an live instance here.

The application runs either:

  • on your workstation as a cross-platform desktop application with the help of the electron framework
  • on your server through docker-compose, where it can make your sequence or profile databases easily accessible over the web

Desktop App

Head over to the release page and download the latest version. We currently support Linux, macOS and Windows.

Adding a search database

Once the app is installed, open the Settings panel. There you can add either sequence databases in FASTA format, such as our Uniclust databases or profile databases in Stockholm format, such as the PFAM.

Web app quickstart with docker-compose

Make sure you have docker (>=17.05), docker-compose (>=1.20.0) and git installed on your server. To start the MMseqs2 web server execute the following commands. Afterwards you can navigate to http://localhost:8877 on a webserver to access the interface.

# clone the repository
git clone https://github.com/soedinglab/MMseqs2-App.git

# navigate to our docker recipes
cd MMseqs2-App/docker-compose

# download the uniclust sequence database
./examples/uniclust/setup.sh

# start the server with docker-compose
docker-compose up

By default, the server will start on port 8877. You can edit the .env file in the docker-compose directory to change this port.

Head over to the Docker recipe readme for more details on running your own server, including how to add your own sequence or profile databases. Take a look at the API documentation to learn how to talk to the server backend.

Building the desktop app

You need to have git, go, node, npm and make installed on your system.

Afterwards run the following commands, and the apps will appear in the build folder.

# clone the repository
git clone https://github.com/soedinglab/MMseqs2-App.git
cd MMseqs2-App

# install all dependencies
npm install

# build the app for all platforms
npm run electron:build
Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].