@jbrowse/cli 1.5.0 → 1.5.4

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
 
@@ -83,17 +83,17 @@ OPTIONS
       type of sequence, by default inferred from sequence file
 
       indexedFasta   An index FASTA (e.g. .fa or .fasta) file;
-                      can optionally specify --faiLocation
+      can optionally specify --faiLocation
 
       bgzipFasta     A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file;
-                      can optionally specify --faiLocation and/or --gziLocation
+      can optionally specify --faiLocation and/or --gziLocation
 
       twoBit         A twoBit (e.g. .2bit) file
 
       chromSizes     A chromosome sizes (e.g. .chrom.sizes) file
 
       custom         Either a JSON file location or inline JSON that defines a custom
-                      sequence adapter; must provide --name if using inline JSON
+      sequence adapter; must provide --name if using inline JSON
 
   --displayName=displayName
       The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier
@@ -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/v1.5.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -194,7 +211,7 @@ EXAMPLES
   /path/to/jb2/installation/config.json
 ```
 
-_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/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/v1.5.0/products/jbrowse-cli/src/commands/add-track.ts)_
+_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/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/v1.5.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -319,7 +336,7 @@ EXAMPLES
   $ jbrowse admin-server -p 8888
 ```
 
-_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -347,14 +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/v1.5.0/products/jbrowse-cli/src/commands/create.ts)_
+_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -371,7 +397,7 @@ OPTIONS
   --all  see all commands in CLI
 ```
 
-_See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v3.2.3/src/commands/help.ts)_
+_See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v3.2.14/src/commands/help.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -408,7 +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/v1.5.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse text-index`
 
@@ -457,14 +483,14 @@ EXAMPLES
   $ jbrowse text-index --out /path/to/jb2/
 
   # indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous
-  index already existed)
+   index already existed)
   $ jbrowse text-index -a hg19 --force
 
   # create index for some files for use in @jbrowse/react-linear-genome-view or similar
   $ 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/v1.5.0/products/jbrowse-cli/src/commands/text-index.ts)_
+_See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -491,14 +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/v1.5.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.4/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.d.ts

@@ -10,9 +10,9 @@ 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';
@@ -79,7 +79,7 @@ export interface Track {
     trackId: string;
     name: string;
     assemblyNames: string[];
-    adapter: Gff3TabixAdapter | GtfTabixAdapter | VcfTabixAdapter;
+    adapter: Gff3TabixAdapter | GtfAdapter | VcfTabixAdapter;
     textSearching?: TextSearching;
 }
 export interface Config {
@@ -97,6 +97,7 @@ interface GithubRelease {
     assets?: [
         {
             browser_download_url: string;
+            name: string;
         }
     ];
 }
@@ -110,7 +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

@@ -118,9 +118,10 @@ class JBrowseCommand extends command_1.default {
     }
     async getLatest() {
         var e_2, _a;
+        var _b;
         try {
-            for (var _b = (0, 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
@@ -128,14 +129,18 @@ 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; }
         }
@@ -159,12 +164,15 @@ class JBrowseCommand extends command_1.default {
         });
     }
     async getTag(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

@@ -5,7 +5,7 @@ const command_1 = require("@oclif/command");
 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 fsPromises = fs_1.default.promises;
+const { rename, copyFile, mkdir, symlink } = fs_1.default.promises;
 function isValidJSON(string) {
     try {
         JSON.parse(string);
@@ -206,7 +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 ? `${output}/config.json` : output;
@@ -347,7 +347,7 @@ class AddAssembly extends base_1.default {
                     if (!filePath) {
                         return undefined;
                     }
-                    return fsPromises.copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
+                    return copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
                 }));
                 return true;
             }
@@ -356,7 +356,7 @@ class AddAssembly extends base_1.default {
                     if (!filePath) {
                         return undefined;
                     }
-                    return fsPromises.symlink(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
+                    return symlink(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
                 }));
                 return true;
             }
@@ -365,7 +365,7 @@ class AddAssembly extends base_1.default {
                     if (!filePath) {
                         return undefined;
                     }
-                    return fsPromises.rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
+                    return rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
                 }));
                 return true;
             }
@@ -379,13 +379,29 @@ class AddAssembly extends base_1.default {
 exports.default = AddAssembly;
 AddAssembly.description = 'Add an assembly to a JBrowse 2 configuration';
 AddAssembly.examples = [
+    '# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory',
     '$ 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-track.d.ts

@@ -42,21 +42,17 @@ export default class AddTrack extends JBrowseCommand {
         index: string;
         index2?: undefined;
     } | {
-        file?: undefined;
+        file: string;
         index?: undefined;
         index2?: undefined;
     } | {
-        file: string;
-        index: undefined;
+        file?: undefined;
+        index?: undefined;
         index2?: undefined;
     } | {
         file: string;
         index: string;
         index2: string;
-    } | {
-        file: string;
-        index?: undefined;
-        index2?: undefined;
     };
     guessAdapter(fileName: string, protocol: string, index?: string): {
         type: string;
@@ -67,7 +63,9 @@ export default class AddTrack extends JBrowseCommand {
         };
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -87,7 +85,9 @@ export default class AddTrack extends JBrowseCommand {
         craiLocation: UriLocation | LocalPathLocation;
         bamLocation?: undefined;
         index?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -103,11 +103,13 @@ export default class AddTrack extends JBrowseCommand {
         pafLocation?: undefined;
     } | {
         type: string;
+        gffLocation: UriLocation | LocalPathLocation;
         bamLocation?: undefined;
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -131,6 +133,30 @@ export default class AddTrack extends JBrowseCommand {
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+    } | {
+        type: string;
+        gtfLocation: UriLocation | LocalPathLocation;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -151,7 +177,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
         bigBedLocation?: undefined;
@@ -174,8 +202,32 @@ export default class AddTrack extends JBrowseCommand {
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        bedGzLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+    } | {
+        type: string;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
         bigBedLocation?: undefined;
         bigWigLocation?: undefined;
@@ -197,7 +249,9 @@ export default class AddTrack extends JBrowseCommand {
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bigBedLocation?: undefined;
@@ -217,7 +271,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -237,7 +293,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -258,7 +316,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -279,7 +339,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -297,7 +359,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -317,7 +381,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -337,7 +403,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -357,7 +425,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -377,7 +447,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;

package/lib/commands/add-track.js

@@ -6,14 +6,16 @@ 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"));
-const fsPromises = fs_1.default.promises;
+const { copyFile, rename, symlink, lstat, unlink } = fs_1.default.promises;
+const { COPYFILE_EXCL } = fs_1.default.constants;
+const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
 class AddTrack extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = this.parse(AddTrack);
         const { track: argsTrack } = runArgs;
         const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, } = runFlags;
         const output = target || out || '.';
-        const isDir = (await fsPromises.lstat(output)).isDirectory();
+        const isDir = (await lstat(output)).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
         let { trackType, trackId, name, assemblyNames } = runFlags;
         const configDirectory = path_1.default.dirname(this.target);
@@ -27,7 +29,6 @@ class AddTrack extends base_1.default {
             }
         }
         const location = argsTrack;
-        const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
         const inPlace = load === 'inPlace';
         const useIndex = isUrl(index) || inPlace || index;
         const effectiveLocation = isUrl(location) || inPlace
@@ -78,11 +79,9 @@ class AddTrack extends base_1.default {
         this.debug(`Assembly name(s) is :${assemblyNames}`);
         const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
         const trackConfig = Object.assign({ type: trackType, trackId,
-            name, category: category ? category.split(',').map(c => c.trim()) : undefined, assemblyNames: assemblyNames.split(',').map(a => a.trim()), adapter }, configObj);
+            name,
+            adapter, category: category === null || category === void 0 ? void 0 : category.split(',').map(c => c.trim()), assemblyNames: assemblyNames.split(',').map(a => a.trim()), description }, configObj);
         this.debug(`Track location: ${location}, index: ${adapter ? adapter.index : ''}`);
-        if (description) {
-            trackConfig.description = description;
-        }
         // any special track modifications go here
         switch (trackType) {
             case 'AlignmentsTrack': {
@@ -113,56 +112,27 @@ class AddTrack extends base_1.default {
         else {
             configContents.tracks.push(trackConfig);
         }
-        // copy/symlinks/moves the track into the jbrowse installation directory
-        const filePaths = Object.values(this.guessFileNames(location, index)).filter(f => !!f);
-        const destinationFn = (dir, file) => path_1.default.join(dir, subDir, path_1.default.basename(file));
-        switch (load) {
-            case 'copy': {
-                await Promise.all(filePaths.map(async (filePath) => {
-                    const dest = destinationFn(configDirectory, filePath);
-                    try {
-                        if (force && fs_1.default.existsSync(dest)) {
-                            await fsPromises.unlink(dest);
-                        }
-                    }
-                    catch (e) {
-                        this.error(e instanceof Error ? e : `${e}`);
-                    }
-                    return fsPromises.copyFile(filePath, dest, fs_1.default.constants.COPYFILE_EXCL);
-                }));
-                break;
-            }
-            case 'symlink': {
-                await Promise.all(filePaths.map(async (filePath) => {
-                    const dest = destinationFn(configDirectory, filePath);
-                    try {
-                        if (force && fs_1.default.existsSync(dest)) {
-                            await fsPromises.unlink(dest);
-                        }
-                    }
-                    catch (e) {
-                        this.error(e instanceof Error ? e : `${e}`);
-                    }
-                    return fsPromises.symlink(filePath, dest);
-                }));
-                break;
+        const filePaths = Object.values(this.guessFileNames(location, index)).filter((f) => !!f);
+        // get path of destination, and remove file at that path if it exists and
+        // force is set
+        const destinationFn = async (dir, file) => {
+            const dest = path_1.default.join(dir, subDir, path_1.default.basename(file));
+            if (force && fs_1.default.existsSync(dest)) {
+                await unlink(dest);
             }
-            case 'move': {
-                await Promise.all(filePaths.map(async (filePath) => {
-                    const dest = destinationFn(configDirectory, filePath);
-                    try {
-                        if (force && fs_1.default.existsSync(dest)) {
-                            await fsPromises.unlink(dest);
-                        }
-                    }
-                    catch (e) {
-                        this.error(e instanceof Error ? e : `${e}`);
-                    }
-                    return fsPromises.rename(filePath, dest);
-                }));
-                break;
+            return dest;
+        };
+        const callbacks = {
+            copy: (src, dest) => copyFile(src, dest, COPYFILE_EXCL),
+            move: (src, dest) => rename(src, dest),
+            symlink: (src, dest) => symlink(src, dest),
+        };
+        await Promise.all(filePaths.map(async (src) => {
+            const dest = await destinationFn(configDirectory, src);
+            if (load === 'copy' || load === 'move' || load === 'symlink') {
+                return callbacks[load](src, dest);
             }
-        }
+        }));
         this.debug(`Writing configuration to file ${this.target}`);
         await this.writeJsonFile(this.target, configContents);
         this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} track "${name}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
@@ -177,28 +147,34 @@ class AddTrack extends base_1.default {
         if (/\.cram$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: `${fileName}.crai`,
+                index: index || `${fileName}.crai`,
             };
         }
         if (/\.gff3?$/i.test(fileName)) {
-            return {};
+            return {
+                file: fileName,
+            };
         }
         if (/\.gff3?\.b?gz$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: `${fileName}.tbi`,
+                index: index || `${fileName}.tbi`,
             };
         }
         if (/\.gtf?$/i.test(fileName)) {
-            return {};
+            return {
+                file: fileName,
+            };
         }
         if (/\.vcf$/i.test(fileName)) {
-            return {};
+            return {
+                file: fileName,
+            };
         }
         if (/\.vcf\.b?gz$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: `${fileName}.tbi`,
+                index: index || `${fileName}.tbi`,
             };
         }
         if (/\.vcf\.idx$/i.test(fileName)) {
@@ -219,13 +195,11 @@ class AddTrack extends base_1.default {
         if (/\.(bb|bigbed)$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: undefined,
             };
         }
         if (/\.(bw|bigwig)$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: undefined,
             };
         }
         if (/\.(fa|fasta|fas|fna|mfa)$/i.test(fileName)) {
@@ -278,7 +252,10 @@ class AddTrack extends base_1.default {
                 return { uri: location, locationType: 'UriLocation' };
             }
             if (protocol === 'localPath') {
-                return { localPath: location, locationType: 'LocalPathLocation' };
+                return {
+                    localPath: location,
+                    locationType: 'LocalPathLocation',
+                };
             }
             throw new Error(`invalid protocol ${protocol}`);
         }
@@ -301,7 +278,8 @@ class AddTrack extends base_1.default {
         }
         if (/\.gff3?$/i.test(fileName)) {
             return {
-                type: 'UNSUPPORTED',
+                type: 'Gff3Adapter',
+                gffLocation: makeLocation(fileName),
             };
         }
         if (/\.gff3?\.b?gz$/i.test(fileName)) {
@@ -316,7 +294,8 @@ class AddTrack extends base_1.default {
         }
         if (/\.gtf?$/i.test(fileName)) {
             return {
-                type: 'UNSUPPORTED',
+                type: 'GtfAdapter',
+                gtfLocation: makeLocation(fileName),
             };
         }
         if (/\.vcf$/i.test(fileName)) {
@@ -439,18 +418,23 @@ class AddTrack extends base_1.default {
 exports.default = AddTrack;
 AddTrack.description = 'Add a track to a JBrowse 2 configuration';
 AddTrack.examples = [
-    `# --load copy copies my.bam and my.bam.bai to current directory and adds track to config.json`,
-    '$ jbrowse add-track /path/to/my.bam --load copy\n',
-    `# same as above, but specify path to bai file`,
-    '$ jbrowse add-track /path/to/my.bam --indexFile /path/to/my.bai --load copy\n',
-    `# --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\n',
-    `# no --load flag to add literal URL for this track to config.json`,
-    '$ jbrowse add-track https://mywebsite.com/my.bam\n',
-    `# --load move to move the file `,
-    `$ jbrowse add-track /path/to/my.bam --name 'New Track' --load move\n`,
-    `# --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`,
+    '# 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',
+    '',
+    '# 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',
+    '',
+    `# 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',
+    '',
+    '# creates symlink for /path/to/my.bam and adds track to config.json',
+    '$ jbrowse add-track /path/to/my.bam --load symlink',
+    '',
+    '# add track from URL to config.json, no --load flag needed',
+    '$ jbrowse add-track https://mywebsite.com/my.bam',
+    '',
+    '# --load inPlace adds a track without doing file operations',
+    '$ jbrowse add-track /url/relative/path.bam --load inPlace',
 ];
 AddTrack.args = [
     {

package/lib/commands/create.js

@@ -60,11 +60,20 @@ class Create extends base_1.default {
 exports.default = Create;
 Create.description = 'Downloads and installs the latest JBrowse 2 release';
 Create.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',
 ];
 Create.args = [
     {

package/lib/commands/text-index.js

@@ -7,10 +7,14 @@ const stream_1 = require("stream");
 const ixixx_1 = require("ixixx");
 const command_1 = require("@oclif/command");
 const gff3Adapter_1 = require("../types/gff3Adapter");
-const gtfAdapter_1 = require("../types/gtfAdapter");
 const vcfAdapter_1 = require("../types/vcfAdapter");
 const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 const common_1 = require("../types/common");
+const object_fromentries_1 = (0, tslib_1.__importDefault)(require("object.fromentries"));
+if (!Object.fromEntries) {
+    // @ts-ignore
+    object_fromentries_1.default.shim();
+}
 function readConf(confFilePath) {
     return JSON.parse(fs_1.default.readFileSync(confFilePath, 'utf8'));
 }
@@ -209,12 +213,10 @@ class TextIndex extends base_1.default {
                 if (type === 'Gff3TabixAdapter') {
                     yield (0, tslib_1.__await)(yield* (0, tslib_1.__asyncDelegator)((0, tslib_1.__asyncValues)((0, gff3Adapter_1.indexGff3)(config, attrs, outLocation, types, quiet))));
                 }
-                else if (type === 'GtfTabixAdapter') {
-                    yield (0, tslib_1.__await)(yield* (0, tslib_1.__asyncDelegator)((0, tslib_1.__asyncValues)((0, gtfAdapter_1.indexGtf)(config, attrs, outLocation, types, quiet))));
-                }
                 else if (type === 'VcfTabixAdapter') {
                     yield (0, tslib_1.__await)(yield* (0, tslib_1.__asyncDelegator)((0, tslib_1.__asyncValues)((0, vcfAdapter_1.indexVcf)(config, attrs, outLocation, types, quiet))));
                 }
+                // gtf unused currently
             }
         });
     }

package/lib/commands/upgrade.d.ts

@@ -3,19 +3,12 @@ import JBrowseCommand from '../base';
 export default class Upgrade extends JBrowseCommand {
     static description: string;
     static examples: string[];
-    static args: ({
+    static args: {
         name: string;
         required: boolean;
         description: string;
         default: string;
-        hidden?: undefined;
-    } | {
-        name: string;
-        required: boolean;
-        description: string;
-        hidden: boolean;
-        default?: undefined;
-    })[];
+    }[];
     static flags: {
         help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
         listVersions: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;

package/lib/commands/upgrade.js

@@ -47,11 +47,23 @@ class Upgrade extends base_1.default {
 exports.default = Upgrade;
 Upgrade.description = 'Upgrades JBrowse 2 to latest version';
 Upgrade.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',
 ];
 Upgrade.args = [
     {
@@ -60,12 +72,6 @@ Upgrade.args = [
         description: `Location where JBrowse 2 is installed`,
         default: '.',
     },
-    {
-        name: 'placeholder',
-        required: false,
-        description: `Placeholder for config file migration scripts`,
-        hidden: true,
-    },
 ];
 Upgrade.flags = {
     help: command_1.flags.help({ char: 'h' }),

package/lib/types/common.js

@@ -58,8 +58,8 @@ function guessAdapterFromFileName(filePath) {
             name,
             assemblyNames: [],
             adapter: {
-                type: 'GtfTabixAdapter',
-                gtfGzLocation: { uri, locationType: 'UriLocation' },
+                type: 'GtfAdapter',
+                gtfLocation: { uri, locationType: 'UriLocation' },
             },
         };
     }
@@ -69,7 +69,7 @@ function guessAdapterFromFileName(filePath) {
 }
 exports.guessAdapterFromFileName = guessAdapterFromFileName;
 function supported(type) {
-    return ['Gff3TabixAdapter', 'GtfTabixAdapter', 'VcfTabixAdapter'].includes(type);
+    return ['Gff3TabixAdapter', 'VcfTabixAdapter'].includes(type);
 }
 exports.supported = supported;
 /**

package/lib/types/gtfAdapter.js

@@ -12,7 +12,7 @@ function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
     return (0, tslib_1.__asyncGenerator)(this, arguments, function* indexGtf_1() {
         var e_1, _a;
         const { adapter, trackId } = config;
-        const { gtfGzLocation: { uri }, } = adapter;
+        const { gtfLocation: { uri }, } = adapter;
         // progress bar code was aided by blog post at
         // https://webomnizz.com/download-a-file-with-progressbar-using-node-js/
         const progressBar = new cli_progress_1.SingleBar({
@@ -67,22 +67,14 @@ function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
                             val.trim().split(',').join(' ').replace(/("|')/g, ''),
                         ];
                     }));
-                    const name = col9Attrs['gene_name'] || '';
-                    const id = col9Attrs['gene_id'] || '';
                     const attrs = attributes
                         .map(attr => col9Attrs[attr])
                         .filter((f) => !!f);
-                    const restAttrs = attributes
-                        .filter(attr => attr !== 'gene_name' && attr !== 'gene_id')
-                        .map(attr => col9Attrs[attr])
-                        .filter((f) => !!f);
-                    if (name || id) {
+                    if (attrs.length) {
                         const record = JSON.stringify([
                             encodeURIComponent(locStr),
                             encodeURIComponent(trackId),
-                            encodeURIComponent(name),
-                            encodeURIComponent(id),
-                            ...restAttrs.map(a => encodeURIComponent(a || '')),
+                            ...attrs.map(a => encodeURIComponent(a || '')),
                         ]).replace(/,/g, '|');
                         yield yield (0, tslib_1.__await)(`${record} ${[...new Set(attrs)].join(' ')}\n`);
                     }

package/oclif.manifest.json

@@ -1 +1 @@
-{"version":"1.5.0","commands":{"add-assembly":{"id":"add-assembly","description":"Add an assembly to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ 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","$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace","$ jbrowse add-assembly GRCh38.config.json --load copy","$ jbrowse add-assembly https://example.com/data/sample.2bit","$ jbrowse add-assembly GRCh38.fa --target /path/to/jb2/installation/customconfig.json --load copy"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of sequence, by default inferred from sequence file\n\nindexedFasta   An index FASTA (e.g. .fa or .fasta) file;\n               can optionally specify --faiLocation\n\nbgzipFasta     A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file;\n               can optionally specify --faiLocation and/or --gziLocation\n\ntwoBit         A twoBit (e.g. .2bit) file\n\nchromSizes     A chromosome sizes (e.g. .chrom.sizes) file\n\ncustom         Either a JSON file location or inline JSON that defines a custom\n               sequence adapter; must provide --name if using inline JSON","options":["indexedFasta","bgzipFasta","twoBit","chromSizes","custom"]},"name":{"name":"name","type":"option","char":"n","description":"Name of the assembly; if not specified, will be guessed using the sequence file name"},"alias":{"name":"alias","type":"option","char":"a","description":"An alias for the assembly name (e.g. \"hg38\" if the name of the assembly is \"GRCh38\");\ncan be specified multiple times"},"displayName":{"name":"displayName","type":"option","description":"The display name to specify for the assembly, e.g. \"Homo sapiens (hg38)\" while the name can be a shorter identifier like \"hg38\""},"faiLocation":{"name":"faiLocation","type":"option","description":"[default: <fastaLocation>.fai] FASTA index file or URL"},"gziLocation":{"name":"gziLocation","type":"option","description":"[default: <fastaLocation>.gzi] FASTA gzip index file or URL"},"refNameAliases":{"name":"refNameAliases","type":"option","description":"Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified"},"refNameAliasesType":{"name":"refNameAliasesType","type":"option","description":"Type of aliases defined by --refNameAliases; if \"custom\", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter","options":["aliases","custom"]},"refNameColors":{"name":"refNameColors","type":"option","description":"A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrite existing assembly if one with the same name exists","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"sequence","description":"sequence file or URL\n\nIf TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai\nand can be optionally specified with --faiLocation\nIf TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be\noptionally specified with --gziLocation","required":true}]},"add-connection":{"id":"add-connection","description":"Add a connection to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-connection http://mysite.com/jbrowse/data/","$ 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\"}, \"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"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom"},"assemblyName":{"name":"assemblyName","type":"option","char":"a","description":"Assembly name of the connection If none, will default to the assembly in your config file"},"config":{"name":"config","type":"option","char":"c","description":"Any extra config settings to add to connection in JSON object format, such as '{\"uri\":\"url\":\"https://sample.com\"}, \"locationType\": \"UriLocation\"}'"},"connectionId":{"name":"connectionId","type":"option","description":"Id for the connection that must be unique to JBrowse.  Defaults to 'connectionType-assemblyName-currentTime'"},"name":{"name":"name","type":"option","char":"n","description":"Name of the connection. Defaults to connectionId if not provided"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the data directory URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites any existing connections if same connection id","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"connectionUrlOrPath","description":"URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ","required":true}]},"add-track-json":{"id":"add-track-json","description":"Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-track-json track.json","$ jbrowse add-track-json track.json --update"],"flags":{"update":{"name":"update","type":"boolean","char":"u","description":"update the contents of an existing track, matched based on trackId","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"}},"args":[{"name":"track","description":"track JSON file or command line arg blob","required":true}]},"add-track":{"id":"add-track","description":"Add a track to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# --load copy copies my.bam and my.bam.bai to current directory and adds track to config.json","$ jbrowse add-track /path/to/my.bam --load copy\n","# same as above, but specify path to bai file","$ jbrowse add-track /path/to/my.bam --indexFile /path/to/my.bai --load copy\n","# --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\n","# no --load flag to add literal URL for this track to config.json","$ jbrowse add-track https://mywebsite.com/my.bam\n","# --load move to move the file ","$ jbrowse add-track /path/to/my.bam --name 'New Track' --load move\n","# --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"],"flags":{"trackType":{"name":"trackType","type":"option","char":"t","description":"Type of track, by default inferred from track file"},"name":{"name":"name","type":"option","char":"n","description":"Name of the track. Will be defaulted to the trackId if none specified"},"indexFile":{"name":"indexFile","type":"option","description":"Optional index file for the track"},"description":{"name":"description","type":"option","char":"d","description":"Optional description of the track"},"assemblyNames":{"name":"assemblyNames","type":"option","char":"a","description":"Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file"},"category":{"name":"category","type":"option","description":"Optional Comma separated string of categories to group tracks"},"config":{"name":"config","type":"option","description":"Any extra config settings to add to a track. i.e '{\"defaultRendering\": \"density\"}'"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"subDir":{"name":"subDir","type":"option","description":"when using --load a file, output to a subdirectory of the target dir","default":""},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"trackId":{"name":"trackId","type":"option","description":"trackId for the track, by default inferred from filename, must be unique throughout config"},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Skip check for whether or not the file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites existing track if it shares the same trackId","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false},"protocol":{"name":"protocol","type":"option","description":"Force protocol to a specific value","default":"uri"}},"args":[{"name":"track","description":"Track file or URL","required":true}]},"admin-server":{"id":"admin-server","description":"Start up a small admin server for JBrowse configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse admin-server","$ jbrowse admin-server -p 8888"],"flags":{"port":{"name":"port","type":"option","char":"p","description":"Specifified port to start the server on;\nDefault is 9090."},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"create":{"id":"create","description":"Downloads and installs the latest JBrowse 2 release","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse create /path/to/new/installation","$ jbrowse create /path/to/new/installation --force","$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip","$ jbrowse create /path/to/new/installation --tag v1.0.0","$ jbrowse create --listVersions # Lists out all available versions of JBrowse 2"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Overwrites existing JBrowse 2 installation if present in path","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 will be installed","required":true}]},"set-default-session":{"id":"set-default-session","description":"Set a default session with views and tracks","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse set-default-session --session /path/to/default/session.json","$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3","$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks","$ jbrowse set-default-session --currentSession # Prints out current default session"],"flags":{"session":{"name":"session","type":"option","char":"s","description":"set path to a file containing session in json format"},"name":{"name":"name","type":"option","char":"n","description":"Give a name for the default session","default":"New Default Session"},"view":{"name":"view","type":"option","char":"v","description":"View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided"},"viewId":{"name":"viewId","type":"option","description":"Identifier for the view. Will be generated on default"},"tracks":{"name":"tracks","type":"option","char":"t","description":"Track id or track ids as comma separated string to put into default session"},"currentSession":{"name":"currentSession","type":"boolean","char":"c","description":"List out the current default session","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to"},"out":{"name":"out","type":"option","description":"synonym for target"},"delete":{"name":"delete","type":"boolean","description":"Delete any existing default session.","allowNo":false},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"text-index":{"id":"text-index","description":"Make a text-indexing file for any given track(s).","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# indexes all tracks that it can find in the current directory's config.json","$ jbrowse text-index","","# indexes specific trackIds that it can find in the current directory's config.json","$ jbrowse text-index --tracks=track1,track2,track3","","# indexes all tracks in a directory's config.json or in a specific config file","$ jbrowse text-index --out /path/to/jb2/","","# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)","$ jbrowse text-index -a hg19 --force","","# create index for some files for use in @jbrowse/react-linear-genome-view or similar","$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"tracks":{"name":"tracks","type":"option","description":"Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks"},"target":{"name":"target","type":"option","description":"Path to config file in JB2 installation directory to read from."},"out":{"name":"out","type":"option","description":"Synonym for target"},"attributes":{"name":"attributes","type":"option","description":"Comma separated list of attributes to index","default":"Name,ID"},"assemblies":{"name":"assemblies","type":"option","char":"a","description":"Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config"},"force":{"name":"force","type":"boolean","description":"Overwrite previously existing indexes","allowNo":false},"quiet":{"name":"quiet","type":"boolean","char":"q","description":"Hide the progress bars","allowNo":false},"perTrack":{"name":"perTrack","type":"boolean","description":"If set, creates an index per track","allowNo":false},"exclude":{"name":"exclude","type":"option","description":"Adds gene type to list of excluded types","default":"CDS,exon"},"file":{"name":"file","type":"option","description":"File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)"},"dryrun":{"name":"dryrun","type":"boolean","description":"Just print out tracks that will be indexed by the process, without doing any indexing","allowNo":false}},"args":[]},"upgrade":{"id":"upgrade","description":"Upgrades JBrowse 2 to latest version","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse upgrade # Upgrades current directory to latest jbrowse release","$ jbrowse upgrade /path/to/jbrowse2/installation","$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0","$ jbrowse upgrade --listVersions # Lists out all available versions of JBrowse 2","$ jbrowse upgrade --url https://sample.com/jbrowse2.zip"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 is installed","required":false,"default":"."},{"name":"placeholder","description":"Placeholder for config file migration scripts","required":false,"hidden":true}]}}}
+{"version":"1.5.4","commands":{"add-assembly":{"id":"add-assembly","description":"Add an assembly to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"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","","# 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","","# 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"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of sequence, by default inferred from sequence file\n\nindexedFasta   An index FASTA (e.g. .fa or .fasta) file;\n               can optionally specify --faiLocation\n\nbgzipFasta     A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file;\n               can optionally specify --faiLocation and/or --gziLocation\n\ntwoBit         A twoBit (e.g. .2bit) file\n\nchromSizes     A chromosome sizes (e.g. .chrom.sizes) file\n\ncustom         Either a JSON file location or inline JSON that defines a custom\n               sequence adapter; must provide --name if using inline JSON","options":["indexedFasta","bgzipFasta","twoBit","chromSizes","custom"]},"name":{"name":"name","type":"option","char":"n","description":"Name of the assembly; if not specified, will be guessed using the sequence file name"},"alias":{"name":"alias","type":"option","char":"a","description":"An alias for the assembly name (e.g. \"hg38\" if the name of the assembly is \"GRCh38\");\ncan be specified multiple times"},"displayName":{"name":"displayName","type":"option","description":"The display name to specify for the assembly, e.g. \"Homo sapiens (hg38)\" while the name can be a shorter identifier like \"hg38\""},"faiLocation":{"name":"faiLocation","type":"option","description":"[default: <fastaLocation>.fai] FASTA index file or URL"},"gziLocation":{"name":"gziLocation","type":"option","description":"[default: <fastaLocation>.gzi] FASTA gzip index file or URL"},"refNameAliases":{"name":"refNameAliases","type":"option","description":"Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified"},"refNameAliasesType":{"name":"refNameAliasesType","type":"option","description":"Type of aliases defined by --refNameAliases; if \"custom\", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter","options":["aliases","custom"]},"refNameColors":{"name":"refNameColors","type":"option","description":"A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrite existing assembly if one with the same name exists","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"sequence","description":"sequence file or URL\n\nIf TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai\nand can be optionally specified with --faiLocation\nIf TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be\noptionally specified with --gziLocation","required":true}]},"add-connection":{"id":"add-connection","description":"Add a connection to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-connection http://mysite.com/jbrowse/data/","$ 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\"}, \"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"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom"},"assemblyName":{"name":"assemblyName","type":"option","char":"a","description":"Assembly name of the connection If none, will default to the assembly in your config file"},"config":{"name":"config","type":"option","char":"c","description":"Any extra config settings to add to connection in JSON object format, such as '{\"uri\":\"url\":\"https://sample.com\"}, \"locationType\": \"UriLocation\"}'"},"connectionId":{"name":"connectionId","type":"option","description":"Id for the connection that must be unique to JBrowse.  Defaults to 'connectionType-assemblyName-currentTime'"},"name":{"name":"name","type":"option","char":"n","description":"Name of the connection. Defaults to connectionId if not provided"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the data directory URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites any existing connections if same connection id","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"connectionUrlOrPath","description":"URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ","required":true}]},"add-track-json":{"id":"add-track-json","description":"Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-track-json track.json","$ jbrowse add-track-json track.json --update"],"flags":{"update":{"name":"update","type":"boolean","char":"u","description":"update the contents of an existing track, matched based on trackId","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"}},"args":[{"name":"track","description":"track JSON file or command line arg blob","required":true}]},"add-track":{"id":"add-track","description":"Add a track to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# 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","","# 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","","# 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","","# creates symlink for /path/to/my.bam and adds track to config.json","$ jbrowse add-track /path/to/my.bam --load symlink","","# add track from URL to config.json, no --load flag needed","$ jbrowse add-track https://mywebsite.com/my.bam","","# --load inPlace adds a track without doing file operations","$ jbrowse add-track /url/relative/path.bam --load inPlace"],"flags":{"trackType":{"name":"trackType","type":"option","char":"t","description":"Type of track, by default inferred from track file"},"name":{"name":"name","type":"option","char":"n","description":"Name of the track. Will be defaulted to the trackId if none specified"},"indexFile":{"name":"indexFile","type":"option","description":"Optional index file for the track"},"description":{"name":"description","type":"option","char":"d","description":"Optional description of the track"},"assemblyNames":{"name":"assemblyNames","type":"option","char":"a","description":"Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file"},"category":{"name":"category","type":"option","description":"Optional Comma separated string of categories to group tracks"},"config":{"name":"config","type":"option","description":"Any extra config settings to add to a track. i.e '{\"defaultRendering\": \"density\"}'"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"subDir":{"name":"subDir","type":"option","description":"when using --load a file, output to a subdirectory of the target dir","default":""},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"trackId":{"name":"trackId","type":"option","description":"trackId for the track, by default inferred from filename, must be unique throughout config"},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Skip check for whether or not the file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites existing track if it shares the same trackId","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false},"protocol":{"name":"protocol","type":"option","description":"Force protocol to a specific value","default":"uri"}},"args":[{"name":"track","description":"Track file or URL","required":true}]},"admin-server":{"id":"admin-server","description":"Start up a small admin server for JBrowse configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse admin-server","$ jbrowse admin-server -p 8888"],"flags":{"port":{"name":"port","type":"option","char":"p","description":"Specifified port to start the server on;\nDefault is 9090."},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"create":{"id":"create","description":"Downloads and installs the latest JBrowse 2 release","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"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","","# List available versions","$ jbrowse create --listVersions"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Overwrites existing JBrowse 2 installation if present in path","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 will be installed","required":true}]},"set-default-session":{"id":"set-default-session","description":"Set a default session with views and tracks","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse set-default-session --session /path/to/default/session.json","$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3","$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks","$ jbrowse set-default-session --currentSession # Prints out current default session"],"flags":{"session":{"name":"session","type":"option","char":"s","description":"set path to a file containing session in json format"},"name":{"name":"name","type":"option","char":"n","description":"Give a name for the default session","default":"New Default Session"},"view":{"name":"view","type":"option","char":"v","description":"View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided"},"viewId":{"name":"viewId","type":"option","description":"Identifier for the view. Will be generated on default"},"tracks":{"name":"tracks","type":"option","char":"t","description":"Track id or track ids as comma separated string to put into default session"},"currentSession":{"name":"currentSession","type":"boolean","char":"c","description":"List out the current default session","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to"},"out":{"name":"out","type":"option","description":"synonym for target"},"delete":{"name":"delete","type":"boolean","description":"Delete any existing default session.","allowNo":false},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"text-index":{"id":"text-index","description":"Make a text-indexing file for any given track(s).","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# indexes all tracks that it can find in the current directory's config.json","$ jbrowse text-index","","# indexes specific trackIds that it can find in the current directory's config.json","$ jbrowse text-index --tracks=track1,track2,track3","","# indexes all tracks in a directory's config.json or in a specific config file","$ jbrowse text-index --out /path/to/jb2/","","# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)","$ jbrowse text-index -a hg19 --force","","# create index for some files for use in @jbrowse/react-linear-genome-view or similar","$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"tracks":{"name":"tracks","type":"option","description":"Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks"},"target":{"name":"target","type":"option","description":"Path to config file in JB2 installation directory to read from."},"out":{"name":"out","type":"option","description":"Synonym for target"},"attributes":{"name":"attributes","type":"option","description":"Comma separated list of attributes to index","default":"Name,ID"},"assemblies":{"name":"assemblies","type":"option","char":"a","description":"Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config"},"force":{"name":"force","type":"boolean","description":"Overwrite previously existing indexes","allowNo":false},"quiet":{"name":"quiet","type":"boolean","char":"q","description":"Hide the progress bars","allowNo":false},"perTrack":{"name":"perTrack","type":"boolean","description":"If set, creates an index per track","allowNo":false},"exclude":{"name":"exclude","type":"option","description":"Adds gene type to list of excluded types","default":"CDS,exon"},"file":{"name":"file","type":"option","description":"File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)"},"dryrun":{"name":"dryrun","type":"boolean","description":"Just print out tracks that will be indexed by the process, without doing any indexing","allowNo":false}},"args":[]},"upgrade":{"id":"upgrade","description":"Upgrades JBrowse 2 to latest version","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# 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","","# 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"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 is installed","required":false,"default":"."}]}}}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "1.5.0",
+  "version": "1.5.4",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -44,25 +44,27 @@
     "docs:version:add": "git add README.md"
   },
   "dependencies": {
-    "@gmod/gff": "^1.1.2",
-    "@oclif/command": "^1",
-    "@oclif/config": "^1",
-    "@oclif/plugin-help": "^3",
+    "@gmod/gff": "^1.2.0",
+    "@oclif/command": "^1.8.11",
+    "@oclif/config": "^1.18.2",
+    "@oclif/errors": "^1",
+    "@oclif/plugin-help": "3.2.14",
     "boxen": "^4.2.0",
     "chalk": "^4.1.0",
     "cli-progress": "^3.9.0",
     "cors": "^2.8.5",
     "express": "^4.17.1",
-    "follow-redirects": "^1.14.1",
-    "ixixx": "^1.0.15",
+    "follow-redirects": "^1.14.6",
+    "ixixx": "^1.0.19",
     "json-parse-better-errors": "^1.0.2",
     "node-fetch": "^2.6.0",
-    "tslib": "^1",
+    "object.fromentries": "^2.0.5",
+    "tslib": "^2.3.1",
     "unzipper": "^0.10.11"
   },
   "devDependencies": {
     "@types/follow-redirects": "^1.13.0",
-    "typescript": "^4.0.0"
+    "typescript": "^4.5.2"
   },
   "oclif": {
     "commands": "./lib/commands",
@@ -75,5 +77,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "542025578a39bd170c8a166f2568ee7edbd54072"
+  "gitHead": "0c398214590969168694b4ed8e20b595178b9efd"
 }

package/CHANGELOG.md

@@ -1,2 +0,0 @@
-- Fixed usage of the `jbrowse upgrade` command having unzipping failures (https://github.com/GMOD/jbrowse-components/pull/1085)
-- Fixed `jbrowse add-track` when there are multiple assemblies (https://github.com/GMOD/jbrowse-components/pull/1103)