@apollo-annotation/cli 0.1.19 → 0.1.21

package/oclif.manifest.json

@@ -12,7 +12,7 @@
           "name": "value"
         }
       },
-      "description": "Use this command to create or edit a user profile with credentials to access\nApollo. Configuration options are:\n\n - address:\nAddress and port e.g http://localhost:3999\n\n- accessType:\nHow to access Apollo. accessType is typically one of: google, microsoft, guest,\nroot. Allowed types depend on your Apollo setup\n\n- accessToken:\nAccess token. Usually inserted by `apollo login`\n\n- rootCredentials.username:\nUsername of root account. Only set this for \"root\" access type\n\n- rootCredentials.password:\nPassword for root account. Only set this for \"root\" access type",
+      "description": "Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:\n\n     - address:\nAddress and port e.g http://localhost:3999\n\n- accessType:\nHow to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your Apollo setup\n\n- accessToken:\nAccess token. Usually inserted by `apollo login`\n\n- rootCredentials.username:\nUsername of root account. Only set this for \"root\" access type\n\n- rootCredentials.password:\nPassword for root account. Only set this for \"root\" access type",
       "examples": [
         {
           "description": "Interactive setup:",
@@ -69,10 +69,10 @@
     "login": {
       "aliases": [],
       "args": {},
-      "description": "Use the provided credentials to obtain and save the token to access Apollo. Once\nthe token for the given profile has been saved in the configuration file, users\ndo not normally need to execute this command again unless the token has expired.\nTo setup a new profile use \"apollo config\"",
+      "description": "Use the provided credentials to obtain and save the token to access Apollo. Once the token for the given profile has been saved in the configuration file, users do not normally need to execute this command again unless the token has expired. To setup a new profile use \"apollo config\"",
       "examples": [
         {
-          "description": "The most basic and probably most typical usage is to login using the default\nprofile in configuration file:",
+          "description": "The most basic and probably most typical usage is to login using the default profile in configuration file:",
           "command": "<%= config.bin %> <%= command.id %>"
         },
         {
@@ -203,7 +203,7 @@
     "status": {
       "aliases": [],
       "args": {},
-      "description": "This command returns \"<profile>: Logged in\" if the selected profile has an\naccess token and \"<profile>: Logged out\" otherwise. Note that this command does\nnot check the validity of the access token.",
+      "description": "This command returns \"<profile>: Logged in\" if the selected profile has an access token and \"<profile>: Logged out\" otherwise.Note that this command does not check the validity of the access token.",
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -236,18 +236,24 @@
         "status.js"
       ]
     },
-    "assembly:add-fasta": {
+    "assembly:add-from-fasta": {
       "aliases": [],
-      "args": {},
-      "description": "Add new assembly from local or external fasta file",
+      "args": {
+        "input": {
+          "description": "Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided.",
+          "name": "input",
+          "required": true
+        }
+      },
+      "description": "Add new assembly. The input fasta may be:\n    * A local file\n    * An external fasta file\n    * The id of a file previously uploaded to Apollo",
       "examples": [
         {
           "description": "From local file:",
-          "command": "<%= config.bin %> <%= command.id %> -i genome.fa -a myAssembly"
+          "command": "<%= config.bin %> <%= command.id %> genome.fa -a myAssembly"
         },
         {
           "description": "From external source we also need the URL of the index:",
-          "command": "<%= config.bin %> <%= command.id %> -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly"
+          "command": "<%= config.bin %> <%= command.id %> https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly"
         }
       ],
       "flags": {
@@ -265,15 +271,6 @@
           "multiple": false,
           "type": "option"
         },
-        "input-file": {
-          "char": "i",
-          "description": "Input fasta file",
-          "name": "input-file",
-          "required": true,
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "assembly": {
           "char": "a",
           "description": "Name for this assembly. Use the file name if omitted",
@@ -282,50 +279,89 @@
           "multiple": false,
           "type": "option"
         },
-        "index": {
-          "char": "x",
-          "description": "URL of the index. Required if input is an external source and ignored if input is a local file",
-          "name": "index",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "force": {
           "char": "f",
           "description": "Delete existing assembly, if it exists",
           "name": "force",
           "allowNo": false,
           "type": "boolean"
+        },
+        "editable": {
+          "char": "e",
+          "description": "Instead of using indexed fasta lookup, the sequence is loaded into the Apollo database and is editable. Use with caution, as editing the sequence often has unintended side effects.",
+          "name": "editable",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "fai": {
+          "description": "Fasta index of the (not-editable) fasta file",
+          "name": "fai",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "gzi": {
+          "description": "Gzi index of the (not-editable) fasta file",
+          "name": "gzi",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "gzip": {
+          "char": "z",
+          "description": "For local file input: Override autodetection and instruct that input is gzip compressed",
+          "exclusive": [
+            "decompressed"
+          ],
+          "name": "gzip",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "decompressed": {
+          "char": "d",
+          "description": "For local file input: Override autodetection and instruct that input is decompressed",
+          "exclusive": [
+            "gzip"
+          ],
+          "name": "decompressed",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "assembly:add-fasta",
+      "id": "assembly:add-from-fasta",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "enableJsonFlag": false,
+      "summary": "Add a new assembly from fasta input",
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "assembly",
-        "add-fasta.js"
+        "add-from-fasta.js"
       ]
     },
-    "assembly:add-gff": {
+    "assembly:add-from-gff": {
       "aliases": [],
-      "args": {},
-      "description": "The gff file is expected to contain sequences as per gff specifications.\nFeatures are also imported by default.",
+      "args": {
+        "input-file": {
+          "description": "Input gff file",
+          "name": "input-file",
+          "required": true
+        }
+      },
+      "description": "The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.",
       "examples": [
         {
           "description": "Import sequences and features:",
-          "command": "<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly"
+          "command": "<%= config.bin %> <%= command.id %> genome.gff -a myAssembly"
         },
         {
           "description": "Import sequences only:",
-          "command": "<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly -o"
+          "command": "<%= config.bin %> <%= command.id %> genome.gff -a myAssembly -o"
         }
       ],
       "flags": {
@@ -343,15 +379,6 @@
           "multiple": false,
           "type": "option"
         },
-        "input-file": {
-          "char": "i",
-          "description": "Input gff or gtf file",
-          "name": "input-file",
-          "required": true,
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "assembly": {
           "char": "a",
           "description": "Name for this assembly. Use the file name if omitted",
@@ -377,25 +404,24 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "assembly:add-gff",
+      "id": "assembly:add-from-gff",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
       "summary": "Add new assembly from gff or gft file",
-      "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "assembly",
-        "add-gff.js"
+        "add-from-gff.js"
       ]
     },
     "assembly:check": {
       "aliases": [],
       "args": {},
-      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible.\nThis command only sets the checks to apply, to retrieve features flagged by\nthese checks use `apollo feature check`.",
+      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible. This command only sets the checks to apply, to retrieve features flagged by these checks use `apollo feature check`.",
       "examples": [
         {
           "description": "View available check types:",
@@ -654,14 +680,59 @@
         "sequence.js"
       ]
     },
+    "change:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "change:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of changes",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "change",
+        "get.js"
+      ]
+    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
-      "description": "See the other commands under `apollo feature` to retrive the parent ID of\ninterest and to populate the child feature with attributes.",
+      "description": "See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature with attributes.",
       "examples": [
         {
           "description": "Add an exon at genomic coordinates 10..20 to this feature ID:",
-          "command": "<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20"
+          "command": "<%= config.bin %> <%= command.id %> -i 660...73f -t exon -s 10 -e 20"
         }
       ],
       "flags": {
@@ -736,7 +807,7 @@
     "feature:check": {
       "aliases": [],
       "args": {},
-      "description": "Use this command to view which features fail checks along with the reason for\nfailing. Use `apollo assembly check` for managing which checks should be applied\nto an assembly",
+      "description": "Use this command to view which features fail checks along with the reason for failing.Use `apollo assembly check` for managing which checks should be applied to an assembly",
       "examples": [
         {
           "description": "Get all check results in the database:",
@@ -799,7 +870,7 @@
     "feature:copy": {
       "aliases": [],
       "args": {},
-      "description": "The feature may be copied to the same or to a different assembly. he destination\nreference sequence may be selected by name only if unique in the database or by\nname and assembly or by identifier.",
+      "description": "The feature may be copied to the same or to a different assembly. The destination reference sequence may be selected by name only if unique in the database or by name and assembly or by identifier.",
       "examples": [
         {
           "description": "Copy this feature ID to chr1:100 in assembly hg38:",
@@ -878,7 +949,7 @@
     "feature:delete": {
       "aliases": [],
       "args": {},
-      "description": "Note that deleting a child feature after deleting its parent will result in an\nerror unless you set -f/--force.",
+      "description": "Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.",
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -940,7 +1011,7 @@
     "feature:edit-attribute": {
       "aliases": [],
       "args": {},
-      "description": "Be aware that there is no checking whether attributes names and values are\nvalid. For example, you can create non-unique ID attributes or you can set gene\nontology terms to non-existing terms",
+      "description": "Be aware that there is no checking whether attributes names and values are valid. For example, you can create non-unique ID attributes or you can set gene ontology terms to non-existing terms",
       "examples": [
         {
           "description": "Add attribute \"domains\" with a list of values:",
@@ -1024,7 +1095,7 @@
     "feature:edit-coords": {
       "aliases": [],
       "args": {},
-      "description": "If editing a child feature that new coordinates must be within the parent's\ncoordinates. To get the identifier of the feature to edit consider using `apollo\nfeature get` or `apollo feature search`",
+      "description": "If editing a child feature that new coordinates must be within the parent's coordinates.To get the identifier of the feature to edit consider using `apollo feature get` or `apollo feature search`",
       "examples": [
         {
           "description": "Edit start and end:",
@@ -1096,7 +1167,7 @@
     "feature:edit-type": {
       "aliases": [],
       "args": {},
-      "description": "Feature type is column 3 in gff format. It must be a valid sequence ontology\nterm although but the valifdity of the new term is not checked.",
+      "description": "Feature type is column 3 in gff format.It must be a valid sequence ontology term although but the valifdity of the new term is not checked.",
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -1150,7 +1221,7 @@
     "feature:edit": {
       "aliases": [],
       "args": {},
-      "description": "Edit a feature by submitting a json input with all the required attributes for\nApollo to process it. This is a very low level command which most users probably\ndo not need.\n\n Input may be a json string or a json file and it may be an array of changes.\nThis is an example input for editing feature type:\n\n {\n \"typeName\": \"TypeChange\",\n \"changedIds\": [\n \"6613f7d22c957525d631b1cc\"\n ],\n \"assembly\": \"6613f7d1360321540a11e5ed\",\n \"featureId\": \"6613f7d22c957525d631b1cc\",\n \"oldType\": \"BAC\",\n \"newType\": \"G_quartet\"\n }",
+      "description": "Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very low level command which most users probably do not need.\n\n    Input may be a json string or a json file and it may be an array of changes. This is an example input for editing feature type:\n\n    {\n      \"typeName\": \"TypeChange\",\n      \"changedIds\": [\n        \"6613f7d22c957525d631b1cc\"\n      ],\n      \"assembly\": \"6613f7d1360321540a11e5ed\",\n      \"featureId\": \"6613f7d22c957525d631b1cc\",\n      \"oldType\": \"BAC\",\n      \"newType\": \"G_quartet\"\n    }",
       "examples": [
         {
           "description": "Editing by passing a json to stdin:",
@@ -1202,7 +1273,7 @@
     "feature:get-id": {
       "aliases": [],
       "args": {},
-      "description": "Invalid identifiers or identifiers not found in the database will be silently\nignored",
+      "description": "Invalid identifiers or identifiers not found in the database will be silently ignored",
       "examples": [
         {
           "description": "Get features for these identifiers:",
@@ -1226,7 +1297,7 @@
         },
         "feature-id": {
           "char": "i",
-          "description": "Retrieves feature with these IDs. Use\n\"-\" to read IDs from stdin (one per\nline)",
+          "description": "Retrieves feature with these IDs. Use \"-\" to read IDs from stdin (one per line)",
           "name": "feature-id",
           "default": [
             "-"
@@ -1263,7 +1334,7 @@
           "command": "<%= config.bin %> <%= command.id %> -a myAssembly"
         },
         {
-          "description": "Get features intersecting chr1:1..1000. You can omit the assembly name if there\nare no other reference sequences named chr1:",
+          "description": "Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences named chr1:",
           "command": "<%= config.bin %> <%= command.id %> -a myAssembly -r chr1 -s 1 -e 1000"
         }
       ],
@@ -1334,12 +1405,18 @@
     },
     "feature:import": {
       "aliases": [],
-      "args": {},
+      "args": {
+        "input-file": {
+          "description": "Input gff file",
+          "name": "input-file",
+          "required": true
+        }
+      },
       "description": "By default, features are added to the existing ones.",
       "examples": [
         {
           "description": "Delete features in myAssembly and then import features.gff3:",
-          "command": "<%= config.bin %> <%= command.id %> -d -i features.gff3 -a myAssembly"
+          "command": "<%= config.bin %> <%= command.id %> features.gff3 -d -a myAssembly"
         }
       ],
       "flags": {
@@ -1357,15 +1434,6 @@
           "multiple": false,
           "type": "option"
         },
-        "input-file": {
-          "char": "i",
-          "description": "Input gff or gtf file",
-          "name": "input-file",
-          "required": true,
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "assembly": {
           "char": "a",
           "description": "Import into this assembly name or assembly ID",
@@ -1391,7 +1459,6 @@
       "pluginType": "core",
       "strict": true,
       "summary": "Import features from local gff file",
-      "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
@@ -1403,7 +1470,7 @@
     "feature:search": {
       "aliases": [],
       "args": {},
-      "description": "Return features matching a query string. This command searches only in:\n\n - Attribute *values* (not attribute names)\n - Source field (which in fact is stored as an attribute)\n - Feature type\n\n The search mode is:\n\n - Case insensitive\n - Match only full words, but not necessarily the full value\n - Common words are ignored. E.g. \"the\", \"with\"\n\n For example, given this feature:\n\n chr1 example SNP 10 30 0.987 . . \"someKey=Fingerprint BAC with reads\"\n\n Queries \"bac\" or \"mRNA\" return the feature. Instead these queries will NOT\nmatch:\n\n - \"someKey\"\n - \"with\"\n - \"Finger\"\n - \"chr1\"\n - \"0.987\"",
+      "description": "Return features matching a query string. This command searches only in:\n\n    - Attribute *values* (not attribute names)\n    - Source field (which in fact is stored as an attribute)\n    - Feature type\n\n    The search mode is:\n\n    - Case insensitive\n    - Match only full words, but not necessarily the full value\n    - Common words are ignored. E.g. \"the\", \"with\"\n\n    For example, given this feature:\n\n    chr1 example SNP 10 30 0.987 . . \"someKey=Fingerprint BAC with reads\"\n\n    Queries \"bac\" or \"mRNA\" return the feature. Instead these queries will NOT match:\n\n    - \"someKey\"\n    - \"with\"\n    - \"Finger\"\n    - \"chr1\"\n    - \"0.987\"",
       "examples": [
         {
           "description": "Search \"bac\" in these assemblies:",
@@ -1436,7 +1503,7 @@
         },
         "assembly": {
           "char": "a",
-          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted\nsearch all assemblies",
+          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
           "name": "assembly",
           "hasDynamicHelp": false,
           "multiple": true,
@@ -1460,10 +1527,16 @@
         "search.js"
       ]
     },
-    "change:get": {
+    "file:delete": {
       "aliases": [],
       "args": {},
-      "description": "Return the change log in json format. Note that when an assembly is deleted the\nlink between common name and ID is lost (it can still be recovered by inspecting\nthe change log but at present this task is left to the user). In such cases you\nneed to use the assembly ID.",
+      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
+      "examples": [
+        {
+          "description": "Delete file multiple files:",
+          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -1479,10 +1552,13 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
+        "file-id": {
+          "char": "i",
+          "description": "IDs of the files to delete",
+          "name": "file-id",
+          "default": [
+            "-"
+          ],
           "hasDynamicHelp": false,
           "multiple": true,
           "type": "option"
@@ -1490,29 +1566,223 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "change:get",
+      "id": "file:delete",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of changes",
+      "summary": "Delete files from the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "change",
+        "file",
+        "delete.js"
+      ]
+    },
+    "file:download": {
+      "aliases": [],
+      "args": {},
+      "description": "See also `apollo file get` to list the files on the server",
+      "examples": [
+        {
+          "description": "Download file with id xyz",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "file-id": {
+          "char": "i",
+          "description": "ID of the file to download",
+          "name": "file-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "output": {
+          "char": "o",
+          "description": "Write output to this file or \"-\" for stdout. Default to the name of the uploaded file.",
+          "name": "output",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:download",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Download a file from the Apollo server",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
+        "download.js"
+      ]
+    },
+    "file:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Print to stdout the list of files in json format",
+      "examples": [
+        {
+          "description": "Get files by id:",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "file-id": {
+          "char": "i",
+          "description": "Get files matching this IDs",
+          "name": "file-id",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of files uploaded to the Apollo server",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
         "get.js"
       ]
     },
-    "refseq:add-alias": {
+    "file:upload": {
+      "aliases": [],
+      "args": {
+        "input-file": {
+          "description": "Local file to upload",
+          "name": "input-file",
+          "required": true
+        }
+      },
+      "description": "This command only uploads a file and returns the corresponding file id.\n  To add an assembly based on this file or to upload & add an assembly in a single pass   see `apollo assembly add-from-fasta` and `add-from-gff`",
+      "examples": [
+        {
+          "description": "Upload local file, type auto-detected:",
+          "command": "<%= config.bin %> <%= command.id %> genome.fa > file.json"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "description": "Set file type or autodetected it if not set.\n        NB: There is no check for whether the file complies to this type",
+          "name": "type",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "options": [
+            "text/x-fasta",
+            "text/x-gff3",
+            "application/x-bgzip-fasta",
+            "text/x-fai",
+            "application/x-gzi"
+          ],
+          "type": "option"
+        },
+        "gzip": {
+          "char": "z",
+          "description": "Override autodetection and instruct that input is gzip compressed",
+          "exclusive": [
+            "decompressed"
+          ],
+          "name": "gzip",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "decompressed": {
+          "char": "d",
+          "description": "Override autodetection and instruct that input is decompressed",
+          "exclusive": [
+            "gzip"
+          ],
+          "name": "decompressed",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:upload",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Upload a local file to the Apollo server",
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
+        "upload.js"
+      ]
+    },
+    "jbrowse:get-config": {
       "aliases": [],
       "args": {},
-      "description": "Reference name aliasing is a process to make chromosomes that are named slightly\ndifferently but which refer to the same thing render properly. This command\nreads a file with reference name aliases and adds them to the database.",
+      "description": "Print to stdout the JBrowse configuration from Apollo in JSON format",
       "examples": [
         {
-          "description": "Add reference name aliases:",
-          "command": "<%= config.bin %> <%= command.id %> -i alias.txt -a myAssembly"
+          "description": "Get JBrowse configuration:",
+          "command": "<%= config.bin %> <%= command.id %> > config.json"
         }
       ],
       "flags": {
@@ -1529,12 +1799,101 @@
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "jbrowse:get-config",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get JBrowse configuration from Apollo",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "jbrowse",
+        "get-config.js"
+      ]
+    },
+    "jbrowse:set-config": {
+      "aliases": [],
+      "args": {
+        "inputFile": {
+          "description": "JBrowse configuration file",
+          "name": "inputFile",
+          "required": true
+        }
+      },
+      "description": "Set JBrowse configuration in Apollo collaboration server",
+      "examples": [
+        {
+          "description": "Add JBrowse configuration:",
+          "command": "<%= config.bin %> <%= command.id %> config.json"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "jbrowse:set-config",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Set JBrowse configuration",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "jbrowse",
+        "set-config.js"
+      ]
+    },
+    "refseq:add-alias": {
+      "aliases": [],
+      "args": {
         "input-file": {
-          "char": "i",
           "description": "Input refname alias file",
           "name": "input-file",
-          "required": true,
+          "required": true
+        }
+      },
+      "description": "Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads a file with reference name aliases and adds them to the database.",
+      "examples": [
+        {
+          "description": "Add reference name aliases:",
+          "command": "<%= config.bin %> <%= command.id %> alias.txt -a myAssembly"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
@@ -1569,7 +1928,7 @@
     "refseq:get": {
       "aliases": [],
       "args": {},
-      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
+      "description": "Output the reference sequences in one or more assemblies in json format. This command returns the sequence characteristics (e.g., name, ID, etc), not the DNA sequences. Use `assembly sequence` for that.",
       "examples": [
         {
           "description": "All sequences in the database:",
@@ -1689,5 +2048,5 @@
       ]
     }
   },
-  "version": "0.1.19"
+  "version": "0.1.21"
 }