From 42c60325d285dbe27f893baaa533ccba81e01575 Mon Sep 17 00:00:00 2001 From: Colin Date: Tue, 6 Jul 2021 23:06:23 -0400 Subject: [PATCH] [update docs] v1.3.2 --- lerna.json | 2 +- packages/core/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/variants/package.json | 2 +- products/jbrowse-cli/README.md | 48 +++++++++---------- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 14 +++--- .../package.json | 10 ++-- products/jbrowse-web/package.json | 14 +++--- 12 files changed, 51 insertions(+), 53 deletions(-) diff --git a/lerna.json b/lerna.json index 4a6f0776b5..6bebda2235 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "1.3.1", + "version": "1.3.2", "npmClient": "yarn", "useWorkspaces": true } diff --git a/packages/core/package.json b/packages/core/package.json index dc05d8bbd0..8c37a23aea 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index 04dfd4529e..a6cf1834b1 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index 6399c0c95e..04e5e22ce7 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -37,7 +37,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.3.4", "@gmod/vcf": "^4.0.0", - "@jbrowse/plugin-variants": "^1.3.1", + "@jbrowse/plugin-variants": "^1.3.2", "@material-ui/icons": "^4.9.1", "classnames": "^2.2.6", "csvtojson": "^2.0.10" diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index 0be4fdeee0..6dbc4719be 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 5c94f8fd75..92a1d49800 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index b377c5978d..8ab8b95c96 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index 2024fd5914..252d2b9348 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -31,16 +31,15 @@ It is likely preferable in most cases to install the tools first however ## Commands - -- [`jbrowse add-assembly SEQUENCE`](#jbrowse-add-assembly-sequence) -- [`jbrowse add-connection CONNECTIONURLORPATH`](#jbrowse-add-connection-connectionurlorpath) -- [`jbrowse add-track TRACK`](#jbrowse-add-track-track) -- [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track) -- [`jbrowse admin-server`](#jbrowse-admin-server) -- [`jbrowse create LOCALPATH`](#jbrowse-create-localpath) -- [`jbrowse help [COMMAND]`](#jbrowse-help-command) -- [`jbrowse set-default-session`](#jbrowse-set-default-session) -- [`jbrowse upgrade [LOCALPATH]`](#jbrowse-upgrade-localpath) +* [`jbrowse add-assembly SEQUENCE`](#jbrowse-add-assembly-sequence) +* [`jbrowse add-connection CONNECTIONURLORPATH`](#jbrowse-add-connection-connectionurlorpath) +* [`jbrowse add-track TRACK`](#jbrowse-add-track-track) +* [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track) +* [`jbrowse admin-server`](#jbrowse-admin-server) +* [`jbrowse create LOCALPATH`](#jbrowse-create-localpath) +* [`jbrowse help [COMMAND]`](#jbrowse-help-command) +* [`jbrowse set-default-session`](#jbrowse-set-default-session) +* [`jbrowse upgrade [LOCALPATH]`](#jbrowse-upgrade-localpath) ## `jbrowse add-assembly SEQUENCE` @@ -71,7 +70,7 @@ OPTIONS show CLI help -l, --load=copy|symlink|move|inPlace - Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data + 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 -n, --name=name @@ -134,7 +133,7 @@ EXAMPLES $ jbrowse add-assembly GRCh38.fa --target /path/to/jb2/installation/customconfig.json --load copy ``` -_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/add-assembly.ts)_ +_See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -180,15 +179,15 @@ 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 + $ 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 + $ 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 https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target + $ 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/v1.3.1/products/jbrowse-cli/src/commands/add-connection.ts)_ +_See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -255,14 +254,14 @@ EXAMPLES # no --load flag to add literal URL for this track to config.json $ jbrowse add-track https://mywebsite.com/my.bam - # --load move to move the file + # --load move to move the file $ jbrowse add-track /path/to/my.bam --name 'New Track' --load move # --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 ``` -_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/add-track.ts)_ +_See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -287,7 +286,7 @@ EXAMPLES $ jbrowse add-track-json track.json --update ``` -_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/add-track-json.ts)_ +_See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -315,7 +314,7 @@ EXAMPLES $ jbrowse admin-server -p 8888 ``` -_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/admin-server.ts)_ +_See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -350,7 +349,7 @@ EXAMPLES $ jbrowse create --listVersions # Lists out all available versions of JBrowse 2 ``` -_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/create.ts)_ +_See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -398,13 +397,13 @@ OPTIONS 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, + $ 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 ``` -_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/set-default-session.ts)_ +_See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -438,8 +437,7 @@ EXAMPLES $ jbrowse upgrade --url https://sample.com/jbrowse2.zip ``` -_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.1/products/jbrowse-cli/src/commands/upgrade.ts)_ - +_See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.3.2/products/jbrowse-cli/src/commands/upgrade.ts)_ ## Debugging diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 6e1b081de8..6b2dda209c 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "1.3.1", + "version": "1.3.2", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 857dd2cf35..50d473d79c 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -36,11 +36,11 @@ "build-electron-only-unpacked:linux": "electron-builder build -l --dir" }, "dependencies": { - "@jbrowse/core": "^1.3.1", + "@jbrowse/core": "^1.3.2", "@jbrowse/plugin-alignments": "^1.3.1", "@jbrowse/plugin-bed": "^1.3.1", "@jbrowse/plugin-breakpoint-split-view": "^1.3.1", - "@jbrowse/plugin-circular-view": "^1.3.1", + "@jbrowse/plugin-circular-view": "^1.3.2", "@jbrowse/plugin-config": "^1.3.1", "@jbrowse/plugin-data-management": "^1.3.1", "@jbrowse/plugin-dotplot-view": "^1.3.1", @@ -54,11 +54,11 @@ "@jbrowse/plugin-menus": "^1.3.1", "@jbrowse/plugin-rdf": "^1.3.1", "@jbrowse/plugin-sequence": "^1.3.1", - "@jbrowse/plugin-spreadsheet-view": "^1.3.1", - "@jbrowse/plugin-sv-inspector": "^1.3.1", - "@jbrowse/plugin-svg": "^1.3.1", + "@jbrowse/plugin-spreadsheet-view": "^1.3.2", + "@jbrowse/plugin-sv-inspector": "^1.3.2", + "@jbrowse/plugin-svg": "^1.3.2", "@jbrowse/plugin-trackhub-registry": "^1.3.0", - "@jbrowse/plugin-variants": "^1.3.1", + "@jbrowse/plugin-variants": "^1.3.2", "@jbrowse/plugin-wiggle": "^1.3.1", "@librpc/web": "rbuels/librpc-web#737bb9706762a52a87169a12c9b59fb241febab0", "@material-ui/core": "^4.9.5", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index 7e0286188a..27ec76e0ab 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "1.3.1", + "version": "1.3.2", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -35,17 +35,17 @@ "postbuild-storybook": "rimraf public/test_data && node scripts/postBuild.js" }, "dependencies": { - "@jbrowse/core": "^1.3.1", + "@jbrowse/core": "^1.3.2", "@jbrowse/plugin-alignments": "^1.3.1", "@jbrowse/plugin-bed": "^1.3.1", - "@jbrowse/plugin-circular-view": "^1.3.1", + "@jbrowse/plugin-circular-view": "^1.3.2", "@jbrowse/plugin-config": "^1.3.1", "@jbrowse/plugin-data-management": "^1.3.1", "@jbrowse/plugin-gff3": "^1.3.0", "@jbrowse/plugin-linear-genome-view": "^1.3.1", "@jbrowse/plugin-sequence": "^1.3.1", - "@jbrowse/plugin-svg": "^1.3.1", - "@jbrowse/plugin-variants": "^1.3.1", + "@jbrowse/plugin-svg": "^1.3.2", + "@jbrowse/plugin-variants": "^1.3.2", "@jbrowse/plugin-wiggle": "^1.3.1", "@material-ui/core": "^4.9.5", "@material-ui/icons": "^4.0.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index 2013eb6816..a2d3d083a9 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "1.3.1", + "version": "1.3.2", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,11 +15,11 @@ "lint": "eslint --ext .js,.ts,.jsx,.tsx src" }, "dependencies": { - "@jbrowse/core": "^1.3.1", + "@jbrowse/core": "^1.3.2", "@jbrowse/plugin-alignments": "^1.3.1", "@jbrowse/plugin-bed": "^1.3.1", "@jbrowse/plugin-breakpoint-split-view": "^1.3.1", - "@jbrowse/plugin-circular-view": "^1.3.1", + "@jbrowse/plugin-circular-view": "^1.3.2", "@jbrowse/plugin-config": "^1.3.1", "@jbrowse/plugin-data-management": "^1.3.1", "@jbrowse/plugin-dotplot-view": "^1.3.1", @@ -33,11 +33,11 @@ "@jbrowse/plugin-menus": "^1.3.1", "@jbrowse/plugin-rdf": "^1.3.1", "@jbrowse/plugin-sequence": "^1.3.1", - "@jbrowse/plugin-spreadsheet-view": "^1.3.1", - "@jbrowse/plugin-sv-inspector": "^1.3.1", - "@jbrowse/plugin-svg": "^1.3.1", + "@jbrowse/plugin-spreadsheet-view": "^1.3.2", + "@jbrowse/plugin-sv-inspector": "^1.3.2", + "@jbrowse/plugin-svg": "^1.3.2", "@jbrowse/plugin-trackhub-registry": "^1.3.0", - "@jbrowse/plugin-variants": "^1.3.1", + "@jbrowse/plugin-variants": "^1.3.2", "@jbrowse/plugin-wiggle": "^1.3.1", "@librpc/web": "rbuels/librpc-web#737bb9706762a52a87169a12c9b59fb241febab0", "@material-ui/core": "^4.9.5",