@jbrowse/cli 1.4.3 → 1.5.2

package/README.md

@@ -4,7 +4,7 @@ id: cli
 toplevel: true
 ---
 
-This document covers the CLI tools.
+This document covers the CLI tools. Note: for @jbrowse/img static export tool, see https://www.npmjs.com/package/@jbrowse/img
 
 ## Installation
 
@@ -131,16 +131,33 @@ OPTIONS
       Creates ./config.json if nonexistent
 
 EXAMPLES
+  # add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and
+  GRCh38.fa.fai to current directory
   $ jbrowse add-assembly GRCh38.fa --load copy
-  $ jbrowse add-assembly GRCh38.fasta.with.custom.extension.xyz --type indexedFasta --load move
-  $ jbrowse add-assembly myFile.fa.gz --name hg38 --alias GRCh38 --displayName "Homo sapiens (hg38)" --load inPlace
+
+  # add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2
+  $ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy
+
+  # force indexedFasta for add-assembly without relying on file extension
+  $ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy
+
+  # add displayName for an assembly
+  $ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"
+
+  # use chrom.sizes file for assembly instead of a fasta file
   $ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace
+
+  # add assembly from preconfigured json file, expert option
   $ jbrowse add-assembly GRCh38.config.json --load copy
+
+  # add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed
   $ jbrowse add-assembly https://example.com/data/sample.2bit
-  $ jbrowse add-assembly GRCh38.fa --target /path/to/jb2/installation/customconfig.json --load copy
+
+  # add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists
+  $ jbrowse add-assembly myfile.fa.gz --load copy
 ```
 
-_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/add-assembly.ts)_
+_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -160,7 +177,7 @@ OPTIONS
                                    file
 
   -c, --config=config              Any extra config settings to add to connection in JSON object format, such as
-                                   '{"uri":"url":"https://sample.com"}}'
+                                   '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'
 
   -f, --force                      Equivalent to `--skipCheck --overwrite`
 
@@ -189,12 +206,12 @@ EXAMPLES
   $ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName
   hg19
   $ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config
-  '{"uri":{"url":"https://mysite.com/path/to/custom"}}' --assemblyName hg19
+  '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' --assemblyName hg19
   $ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target
   /path/to/jb2/installation/config.json
 ```
 
-_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/add-connection.ts)_
+_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -249,26 +266,26 @@ OPTIONS
                                         throughout config
 
 EXAMPLES
-  # --load copy copies my.bam and my.bam.bai to current directory and adds track to config.json
+  # copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json
   $ jbrowse add-track /path/to/my.bam --load copy
 
-  # same as above, but specify path to bai file
-  $ jbrowse add-track /path/to/my.bam --indexFile /path/to/my.bai --load copy
+  # copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json
+  $ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam
 
-  # --load symlink creates symlink in /path/to/jb2/ directory for this file, and adds track to config.json
-  $ jbrowse add-track /path/to/my.bam --target /path/to/jb2/config.json --load symlink
+  # same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai
+  $ jbrowse add-track my.bam --indexFile my.bai --load copy
 
-  # no --load flag to add literal URL for this track to config.json
-  $ jbrowse add-track https://mywebsite.com/my.bam
+  # creates symlink for /path/to/my.bam and adds track to config.json
+  $ jbrowse add-track /path/to/my.bam --load symlink
 
-  # --load move to move the file
-  $ jbrowse add-track /path/to/my.bam --name 'New Track' --load move
+  # add track from URL to config.json, no --load flag needed
+  $ jbrowse add-track https://mywebsite.com/my.bam
 
-  # --load inPlace puts /url/relative/path.bam in the config without performing any file operations
-  $ jbrowse add-track /url/relative/path.bam --trackId AlignmentsTrack1 --load url --overwrite
+  # --load inPlace adds a track without doing file operations
+  $ jbrowse add-track /url/relative/path.bam --load inPlace
 ```
 
-_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/add-track.ts)_
+_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -293,7 +310,7 @@ EXAMPLES
   $ jbrowse add-track-json track.json --update
 ```
 
-_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/add-track-json.ts)_
+_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -311,8 +328,6 @@ OPTIONS
 
   --out=out        synonym for target
 
-  --skipCheck      Don't check whether or not you are in a JBrowse directory
-
   --target=target  path to config file in JB2 installation directory to write out to.
                    Creates ./config.json if nonexistent
 
@@ -321,7 +336,7 @@ EXAMPLES
   $ jbrowse admin-server -p 8888
 ```
 
-_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/admin-server.ts)_
+_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -349,14 +364,23 @@ OPTIONS
   --nightly           Download the latest development build from the main branch
 
 EXAMPLES
+  # Download latest release from github, and put in specific path
   $ jbrowse create /path/to/new/installation
+
+  # Download latest release from github and force overwrite existing contents at path
   $ jbrowse create /path/to/new/installation --force
+
+  # Download latest release from a specific URL
   $ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip
+
+  # Download a specific tag from github
   $ jbrowse create /path/to/new/installation --tag v1.0.0
-  $ jbrowse create --listVersions # Lists out all available versions of JBrowse 2
+
+  # List available versions
+  $ jbrowse create --listVersions
 ```
 
-_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/create.ts)_
+_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -373,7 +397,7 @@ OPTIONS
   --all  see all commands in CLI
 ```
 
-_See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v3.2.0/src/commands/help.ts)_
+_See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v3.2.3/src/commands/help.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -410,7 +434,7 @@ EXAMPLES
   $ jbrowse set-default-session --currentSession # Prints out current default session
 ```
 
-_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/set-default-session.ts)_
+_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse text-index`
 
@@ -466,7 +490,7 @@ EXAMPLES
   $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
 ```
 
-_See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/text-index.ts)_
+_See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -493,14 +517,26 @@ OPTIONS
   --nightly           Download the latest development build from the main branch
 
 EXAMPLES
-  $ jbrowse upgrade # Upgrades current directory to latest jbrowse release
+  # Upgrades current directory to latest jbrowse release
+  $ jbrowse upgrade
+
+  # Upgrade jbrowse instance at a specific filesystem path
   $ jbrowse upgrade /path/to/jbrowse2/installation
+
+  # Upgrade to a specific tag
   $ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0
-  $ jbrowse upgrade --listVersions # Lists out all available versions of JBrowse 2
+
+  # List versions available on github
+  $ jbrowse upgrade --listVersions
+
+  # Upgrade from a specific URL
   $ jbrowse upgrade --url https://sample.com/jbrowse2.zip
+
+  # Get nightly release from main branch
+  $ jbrowse upgrade --nightly
 ```
 
-_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.4.3/products/jbrowse-cli/src/commands/upgrade.ts)_
+_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.d.ts

@@ -4,14 +4,15 @@
 import Command from '@oclif/command';
 export interface UriLocation {
     uri: string;
+    locationType: 'UriLocation';
 }
 export interface Gff3TabixAdapter {
     type: 'Gff3TabixAdapter';
     gffGzLocation: UriLocation;
 }
-export interface GtfTabixAdapter {
-    type: 'GtfTabixAdapter';
-    gtfGzLocation: UriLocation;
+export interface GtfAdapter {
+    type: 'GtfAdapter';
+    gtfLocation: UriLocation;
 }
 export interface VcfTabixAdapter {
     type: 'VcfTabixAdapter';
@@ -78,7 +79,7 @@ export interface Track {
     trackId: string;
     name: string;
     assemblyNames: string[];
-    adapter: Gff3TabixAdapter | GtfTabixAdapter | VcfTabixAdapter;
+    adapter: Gff3TabixAdapter | GtfAdapter | VcfTabixAdapter;
     textSearching?: TextSearching;
 }
 export interface Config {
@@ -93,9 +94,12 @@ export interface Config {
 interface GithubRelease {
     tag_name: string;
     prerelease: boolean;
-    assets?: [{
-        browser_download_url: string;
-    }];
+    assets?: [
+        {
+            browser_download_url: string;
+            name: string;
+        }
+    ];
 }
 export default abstract class JBrowseCommand extends Command {
     init(): Promise<void>;
@@ -107,7 +111,7 @@ export default abstract class JBrowseCommand extends Command {
     fetchGithubVersions(): Promise<GithubRelease[]>;
     getLatest(): Promise<string>;
     fetchVersions(): AsyncGenerator<GithubRelease[], void, unknown>;
-    getTag(tag: string): Promise<any>;
+    getTag(tag: string): Promise<string>;
     getBranch(branch: string): Promise<string>;
 }
 export {};

package/lib/base.js

@@ -4,11 +4,11 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
-const command_1 = tslib_1.__importDefault(require("@oclif/command"));
+const command_1 = (0, tslib_1.__importDefault)(require("@oclif/command"));
 const fs_1 = require("fs");
-const path_1 = tslib_1.__importDefault(require("path"));
-const json_parse_better_errors_1 = tslib_1.__importDefault(require("json-parse-better-errors"));
-const node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const json_parse_better_errors_1 = (0, tslib_1.__importDefault)(require("json-parse-better-errors"));
+const node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
 class JBrowseCommand extends command_1.default {
     async init() { }
     async readFile(location) {
@@ -20,7 +20,7 @@ class JBrowseCommand extends command_1.default {
             contents = await fs_1.promises.readFile(location, { encoding: 'utf8' });
         }
         catch (error) {
-            this.error(error instanceof Error ? error : error.message, {
+            this.error(error instanceof Error ? error : `${error}`, {
                 suggestions: [
                     `Make sure the file "${location}" exists or use --out to point to a directory with a config.json`,
                     'Run `jbrowse add-assembly` to create a config file',
@@ -30,10 +30,10 @@ class JBrowseCommand extends command_1.default {
         }
         let result;
         try {
-            result = json_parse_better_errors_1.default(contents);
+            result = (0, json_parse_better_errors_1.default)(contents);
         }
         catch (error) {
-            this.error(error instanceof Error ? error : error.message, {
+            this.error(error instanceof Error ? error : `${error}`, {
                 suggestions: [`Make sure "${location}" is a valid JSON file`],
                 exit: 50,
             });
@@ -55,7 +55,7 @@ class JBrowseCommand extends command_1.default {
         }
         if (locationUrl) {
             if (check) {
-                const response = await node_fetch_1.default(locationUrl, { method: 'HEAD' });
+                const response = await (0, node_fetch_1.default)(locationUrl, { method: 'HEAD' });
                 if (!response.ok) {
                     throw new Error(`${locationUrl} result ${response.statusText}`);
                 }
@@ -89,7 +89,7 @@ class JBrowseCommand extends command_1.default {
         let result;
         // see if it's inline JSON
         try {
-            result = json_parse_better_errors_1.default(inlineOrFileName);
+            result = (0, json_parse_better_errors_1.default)(inlineOrFileName);
         }
         catch (error) {
             this.debug(`Not valid inline JSON, attempting to parse as filename: '${inlineOrFileName}'`);
@@ -102,7 +102,7 @@ class JBrowseCommand extends command_1.default {
         var e_1, _a;
         let versions = [];
         try {
-            for (var _b = tslib_1.__asyncValues(this.fetchVersions()), _c; _c = await _b.next(), !_c.done;) {
+            for (var _b = (0, tslib_1.__asyncValues)(this.fetchVersions()), _c; _c = await _b.next(), !_c.done;) {
                 const iter = _c.value;
                 versions = versions.concat(iter);
             }
@@ -118,9 +118,10 @@ class JBrowseCommand extends command_1.default {
     }
     async getLatest() {
         var e_2, _a;
+        var _b;
         try {
-            for (var _b = tslib_1.__asyncValues(this.fetchVersions()), _c; _c = await _b.next(), !_c.done;) {
-                const versions = _c.value;
+            for (var _c = (0, tslib_1.__asyncValues)(this.fetchVersions()), _d; _d = await _c.next(), !_d.done;) {
+                const versions = _d.value;
                 // if a release was just uploaded, or an erroneous build was made
                 // then it might have no build asset
                 const nonprereleases = versions
@@ -128,28 +129,32 @@ class JBrowseCommand extends command_1.default {
                     .filter(release => release.assets && release.assets.length > 0);
                 if (nonprereleases.length !== 0) {
                     // @ts-ignore
-                    return nonprereleases[0].assets[0].browser_download_url;
+                    const file = (_b = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))) === null || _b === void 0 ? void 0 : _b.browser_download_url;
+                    if (!file) {
+                        throw new Error('no jbrowse-web download found');
+                    }
+                    return file;
                 }
             }
         }
         catch (e_2_1) { e_2 = { error: e_2_1 }; }
         finally {
             try {
-                if (_c && !_c.done && (_a = _b.return)) await _a.call(_b);
+                if (_d && !_d.done && (_a = _c.return)) await _a.call(_c);
             }
             finally { if (e_2) throw e_2.error; }
         }
         throw new Error('no version tags found');
     }
     fetchVersions() {
-        return tslib_1.__asyncGenerator(this, arguments, function* fetchVersions_1() {
+        return (0, tslib_1.__asyncGenerator)(this, arguments, function* fetchVersions_1() {
             let page = 1;
             let result;
             do {
-                const response = yield tslib_1.__await(node_fetch_1.default(`https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`));
+                const response = yield (0, tslib_1.__await)((0, node_fetch_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`));
                 if (response.ok) {
-                    result = (yield tslib_1.__await(response.json()));
-                    yield yield tslib_1.__await(result.filter(release => release.tag_name.startsWith('v')));
+                    result = (yield (0, tslib_1.__await)(response.json()));
+                    yield yield (0, tslib_1.__await)(result.filter(release => release.tag_name.startsWith('v')));
                     page++;
                 }
                 else {
@@ -159,12 +164,15 @@ class JBrowseCommand extends command_1.default {
         });
     }
     async getTag(tag) {
-        const response = await node_fetch_1.default(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
+        var _a, _b;
+        const response = await (0, node_fetch_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
         if (response.ok) {
-            const result = await response.json();
-            return result && result.assets
-                ? result.assets[0].browser_download_url
-                : this.error('Could not find version specified. Use --listVersions to see all available versions', { exit: 90 });
+            const result = (await response.json());
+            const file = (_b = (_a = result === null || result === void 0 ? void 0 : result.assets) === null || _a === void 0 ? void 0 : _a.find(f => f.name.includes('jbrowse-web'))) === null || _b === void 0 ? void 0 : _b.browser_download_url;
+            if (!file) {
+                this.error('Could not find version specified. Use --listVersions to see all available versions', { exit: 90 });
+            }
+            return file;
         }
         return this.error(`Error: Could not find version: ${response.statusText}`, {
             exit: 90,

package/lib/commands/add-assembly.js

@@ -2,10 +2,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const base_1 = tslib_1.__importDefault(require("../base"));
-const fsPromises = fs_1.default.promises;
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
+const { rename, copyFile, mkdir, symlink } = fs_1.default.promises;
 function isValidJSON(string) {
     try {
         JSON.parse(string);
@@ -68,8 +68,11 @@ class AddAssembly extends base_1.default {
                     trackId: `${name}-ReferenceSequenceTrack`,
                     adapter: {
                         type: 'IndexedFastaAdapter',
-                        fastaLocation: { uri: sequenceLocation },
-                        faiLocation: { uri: indexLocation },
+                        fastaLocation: {
+                            uri: sequenceLocation,
+                            locationType: 'UriLocation',
+                        },
+                        faiLocation: { uri: indexLocation, locationType: 'UriLocation' },
                     },
                 };
                 break;
@@ -107,9 +110,15 @@ class AddAssembly extends base_1.default {
                     trackId: `${name}-ReferenceSequenceTrack`,
                     adapter: {
                         type: 'BgzipFastaAdapter',
-                        fastaLocation: { uri: sequenceLocation },
-                        faiLocation: { uri: indexLocation },
-                        gziLocation: { uri: bgzipIndexLocation },
+                        fastaLocation: {
+                            uri: sequenceLocation,
+                            locationType: 'UriLocation',
+                        },
+                        faiLocation: { uri: indexLocation, locationType: 'UriLocation' },
+                        gziLocation: {
+                            uri: bgzipIndexLocation,
+                            locationType: 'UriLocation',
+                        },
                     },
                 };
                 break;
@@ -132,7 +141,10 @@ class AddAssembly extends base_1.default {
                     trackId: `${name}-ReferenceSequenceTrack`,
                     adapter: {
                         type: 'TwoBitAdapter',
-                        twoBitLocation: { uri: sequenceLocation },
+                        twoBitLocation: {
+                            uri: sequenceLocation,
+                            locationType: 'UriLocation',
+                        },
                     },
                 };
                 break;
@@ -155,7 +167,10 @@ class AddAssembly extends base_1.default {
                     trackId: `${name}-ReferenceSequenceTrack`,
                     adapter: {
                         type: 'ChromSizesAdapter',
-                        chromSizesLocation: { uri: sequenceLocation },
+                        chromSizesLocation: {
+                            uri: sequenceLocation,
+                            locationType: 'UriLocation',
+                        },
                     },
                 };
                 break;
@@ -191,7 +206,7 @@ class AddAssembly extends base_1.default {
         const { args: runArgs, flags: runFlags } = this.parse(AddAssembly);
         const output = runFlags.target || runFlags.out || '.';
         if (!(await exists(output))) {
-            await fsPromises.mkdir(output, { recursive: true });
+            await mkdir(output, { recursive: true });
         }
         const isDir = fs_1.default.statSync(output).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
@@ -228,7 +243,10 @@ class AddAssembly extends base_1.default {
                 assembly.refNameAliases = {
                     adapter: {
                         type: 'RefNameAliasAdapter',
-                        location: { uri: refNameAliasesLocation },
+                        location: {
+                            uri: refNameAliasesLocation,
+                            locationType: 'UriLocation',
+                        },
                     },
                 };
             }
@@ -329,7 +347,7 @@ class AddAssembly extends base_1.default {
                     if (!filePath) {
                         return undefined;
                     }
-                    return fsPromises.copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
+                    return copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
                 }));
                 return true;
             }
@@ -338,7 +356,7 @@ class AddAssembly extends base_1.default {
                     if (!filePath) {
                         return undefined;
                     }
-                    return fsPromises.symlink(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
+                    return symlink(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
                 }));
                 return true;
             }
@@ -347,7 +365,7 @@ class AddAssembly extends base_1.default {
                     if (!filePath) {
                         return undefined;
                     }
-                    return fsPromises.rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
+                    return rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
                 }));
                 return true;
             }
@@ -361,13 +379,29 @@ class AddAssembly extends base_1.default {
 exports.default = AddAssembly;
 AddAssembly.description = 'Add an assembly to a JBrowse 2 configuration';
 AddAssembly.examples = [
+    '# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory',
     '$ jbrowse add-assembly GRCh38.fa --load copy',
-    '$ jbrowse add-assembly GRCh38.fasta.with.custom.extension.xyz --type indexedFasta --load move',
-    '$ jbrowse add-assembly myFile.fa.gz --name hg38 --alias GRCh38 --displayName "Homo sapiens (hg38)" --load inPlace',
+    '',
+    '# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2',
+    '$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy',
+    '',
+    '# force indexedFasta for add-assembly without relying on file extension',
+    '$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy',
+    '',
+    '# add displayName for an assembly',
+    '$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"',
+    '',
+    '# use chrom.sizes file for assembly instead of a fasta file',
     '$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace',
+    '',
+    '# add assembly from preconfigured json file, expert option',
     '$ jbrowse add-assembly GRCh38.config.json --load copy',
+    '',
+    '# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed',
     '$ jbrowse add-assembly https://example.com/data/sample.2bit',
-    '$ jbrowse add-assembly GRCh38.fa --target /path/to/jb2/installation/customconfig.json --load copy',
+    '',
+    '# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists',
+    '$ jbrowse add-assembly myfile.fa.gz --load copy',
 ];
 AddAssembly.args = [
     {

package/lib/commands/add-connection.js

@@ -2,17 +2,16 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const json_parse_better_errors_1 = tslib_1.__importDefault(require("json-parse-better-errors"));
-const base_1 = tslib_1.__importDefault(require("../base"));
-const fsPromises = fs_1.default.promises;
+const node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const json_parse_better_errors_1 = (0, tslib_1.__importDefault)(require("json-parse-better-errors"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 class AddConnection extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = this.parse(AddConnection);
         const output = runFlags.target || runFlags.out || '.';
-        const isDir = (await fsPromises.lstat(output)).isDirectory();
+        const isDir = fs_1.default.lstatSync(output).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
         const { connectionUrlOrPath: argsPath } = runArgs;
         const { config } = runFlags;
@@ -56,7 +55,7 @@ class AddConnection extends base_1.default {
         let configObj = {};
         if (config) {
             try {
-                configObj = json_parse_better_errors_1.default(config);
+                configObj = (0, json_parse_better_errors_1.default)(config);
             }
             catch (error) {
                 this.error('Could not parse provided JSON object');
@@ -66,11 +65,17 @@ class AddConnection extends base_1.default {
             connectionId, name: name || connectionId, assemblyName }, configObj);
         switch (type) {
             case 'UCSCTrackHubConnection': {
-                connectionConfig.hubTxtLocation = { uri: url };
+                connectionConfig.hubTxtLocation = {
+                    uri: url,
+                    locationType: 'UriLocation',
+                };
                 break;
             }
             case 'JBrowse1Connection': {
-                connectionConfig.dataDirLocation = { uri: url };
+                connectionConfig.dataDirLocation = {
+                    uri: url,
+                    locationType: 'UriLocation',
+                };
                 break;
             }
             default: {
@@ -113,7 +118,7 @@ class AddConnection extends base_1.default {
             let response;
             try {
                 if (check) {
-                    response = await node_fetch_1.default(locationUrl, { method: 'HEAD' });
+                    response = await (0, node_fetch_1.default)(locationUrl, { method: 'HEAD' });
                 }
                 if (!response || response.ok) {
                     return locationUrl.href;
@@ -158,7 +163,7 @@ AddConnection.examples = [
     '$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection',
     '$ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19',
     '$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName hg19',
-    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}}' --assemblyName hg19`,
+    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' --assemblyName hg19`,
     '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
 ];
 AddConnection.args = [
@@ -179,7 +184,7 @@ AddConnection.flags = {
     }),
     config: command_1.flags.string({
         char: 'c',
-        description: `Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}}'`,
+        description: `Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'`,
     }),
     connectionId: command_1.flags.string({
         description: `Id for the connection that must be unique to JBrowse.  Defaults to 'connectionType-assemblyName-currentTime'`,

package/lib/commands/add-track-json.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
 const fs_1 = require("fs");
-const base_1 = tslib_1.__importDefault(require("../base"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 class AddTrackJson extends base_1.default {
     async run() {
         const { args, flags: runFlags } = this.parse(AddTrackJson);