Merge branch 'master' of https://github.com/soedinglab/MMseqs2-App

Author: rachelse

backend/config.json

@@ -0,0 +1,162 @@
+{
+	// One of: mmseqs,foldseek,colabfold,predictprotein
+	"app": "foldseek",
+    // should mmseqs und webserver output be printed
+    "verbose": true,
+    "server" : {
+        "address"    : "127.0.0.1:8081",
+        // 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 (used additional CPUs)
+        "paralleldatabases": 1,
+    },
+    // paths to workfolders and mmseqs, special character ~ is resolved relative to the binary location
+    "paths" : {
+        // path to mmseqs databases, has to be shared between server/workers
+        "databases"    : "../resources/databases",
+        // path to job results and scratch directory, has to be shared between server/workers
+        "results"      : "../resources/jobs",
+        // temporary files for index building
+        "temporary"    : "../resources/tmp",
+        /*
+        // 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
+            "parallelstages": false,
+            // paths for search databases
+            "uniref"        : "~databases/uniref30_2103",
+            "pdb"           : "~databases/pdb70",
+            "environmental" : "~databases/colabfold_envdb_202108",
+			"environmentalpair" : "~databases/spire_ctg10_2401_db",
+            // paths for templates
+            "pdb70"         : "~databases/pdb70",
+            "pdbdivided"    : "~databases/pdbdivided",
+            "pdbobsolete"   : "~databases/pdbobsolete",
+        },
+        */
+        // path to foldseek binary
+        "foldseek"     : "../resources/mac/foldseek",
+        "foldseekinterface" : "../resources/mac/foldseek",
+        "foldmason"    : "../resources/mac/foldmason",
+		"folddisco"    : "../resources/mac/folddisco",
+		"foldcomp"     : "../resources/mac/foldcomp",
+		"pdb100"       : "~pdb100",
+        // 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" : {
+        "mailer" : {
+            // three types available:
+            // null: uses NullTransport class, which ignores all sent emails
+            "type" : "null"
+            /* smtp: Uses SMTP to send emails example for gmail
+            "type" : "smtp",
+            "transport" : {
+                // full host URL with port
+                "host" : "smtp.gmail.com:587",
+                // RFC 4616  PLAIN authentication
+                "auth" : {
+                    {
+                        // empty for gmail
+                        "identity" : "",
+                        // gmail user
+                        "username" : "user@gmail.com",
+                        "password" : "password",
+                        "host" : "smtp.gmail.com",
+                    },
+                },
+            },
+            */
+            /* mailgun: Uses the mailgun API to send emails
+            "type"      : "mailgun",
+            "transport" : {
+                // mailgun domain
+                "domain" : "mail.mmseqs.com",
+                // mailgun API private key
+                "secretkey" : "key-XXXX",
+                // mailgun API public key
+                "publickey" : "pubkey-XXXX",
+            },
+            */
+        },
+        // Email FROM field
+        "sender"    : "mail@example.org",
+        /* Bracket notation is also possible:
+        "sender"    : "Webserver <mail@example.org>",
+        */
+        // Email templates. First "%s" is resolved to the ticket identifier
+        "templates" : {
+            "success" : {
+                "subject" : "Done -- %s",
+                "body"    : "%s",
+            },
+            "timeout" : {
+                "subject" : "Timeout -- %s",
+                "body"    : "%s",
+            },
+            "error"   : {
+                "subject" : "Error -- %s",
+                "body"    : "%s",
+            }
+        }
+    }
+}