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| { | |
| "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" | |
| } | |
| } | |
| } | |
| } | |