{ "app": "colabfold", // should mmseqs und webserver output be printed "verbose": true, "server" : { "address" : "127.0.0.1:8080", // prefix for all API endpoints "pathprefix" : "/api/", // enables additional API endpoints for adding databases // WARNING: No additional authentication provided. Enable only within trusted network/for trusted admins. "dbmanagment": false, /* enable HTTP Basic Auth (optional) "auth": { "username" : "", "password" : "", }, // enable rate-limiting (optional) "ratelimit" : { // this uses the token-bucket algorithm // i.e. we start with a full bucket (with burst tokens) and refill it at a given rate // each request consumes one token, if the bucket is empty the request is rejected // the example below starts with 20 tokens and refills 0.0333 token per second (2 tokens per minute) "rate" : 0.03333333333333, "burst" : 20, "ttl" : 1, "reason" : "The foldseek server is a shared resource. Please be mindful about submitting many jobs.", // CIDRs to allow without rate-limiting "allowlist": [], }, */ // should CORS headers be set to allow requests from anywhere "cors" : true, // should old jobs be checked on startup "checkold" : true, }, "worker": { // should workers exit immediately after SIGINT/SIGTERM signal or gracefully wait for job completion "gracefulexit": false, // How many databases can be searched in parallel (uses additional CPUs) "paralleldatabases": 1, }, // paths to workfolders and mmseqs, special character ~ is resolved relative to the binary location "paths" : { // path to job results and scratch directory, has to be shared between server/workers "results" : "~jobs", // paths to colabfold templates "colabfold" : { // configure GPU support for colabfold // GPU support for mmseqs and foldseek is configured in database .params files /* "gpu" : { // enable/disable "gpu": true, // enable gpuserver, saves about 1.5s per request in overhead "server": true, // set cuda visible devices for all databases, can be empty/omitted // "devices": "0,1,2", // set/override devices per database for better VRAM managment // "uniref_devices": "0", // "pdb_devices": "1", // "environmental_devices": "2", }, */ // should stages be run in parallel, faster at the cost of more CPU "parallelstages": false, // paths for search databases "uniref" : "~databases/uniref30_2302_db", "pdb" : "~databases/pdb100_230517", "environmental" : "~databases/colabfold_envdb_202108_db", // not used in public MSA server // "environmentalpair" : "~databases/spire_ctg10_2401_db", // paths for templates "pdb70" : "~databases/pdb100", "pdbdivided" : "~databases/pdb/divided", "pdbobsolete" : "~databases/pdb/obsolete", }, // path to mmseqs binary "mmseqs" : "mmseqs", }, // connection details for redis database, not used in -local mode "redis" : { "network" : "tcp", "address" : "localhost:6379", "password" : "", "index" : 0, }, // options for local/single-binary server "local" : { "workers" : 1, // should old jobs be checked on startup "checkold" : true, }, "mail" : { "type" : "null", "sender" : "mail@example.org", "templates" : { "success" : { "subject" : "Done -- %s", "body" : "Dear User,\nThe results of your submitted job are available now at https://search.mmseqs.com/queue/%s .\n" }, "timeout" : { "subject" : "Timeout -- %s", "body" : "Dear User,\nYour submitted job timed out. More details are available at https://search.mmseqs.com/queue/%s .\nPlease adjust the job and submit it again.\n" }, "error" : { "subject" : "Error -- %s", "body" : "Dear User,\nYour submitted job failed. More details are available at https://search.mmseqs.com/queue/%s .\nPlease submit your job later again.\n" } } } }