Mercurial > repos > fubar > jbrowse2
changeset 10:c60b17456297 draft
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
| author | fubar |
|---|---|
| date | Sat, 20 Jan 2024 07:13:26 +0000 |
| parents | a26c41e304c3 |
| children | f5ce31c2f47d |
| files | 4f27993eab7751041e8c72047be3ea53_0.bw all_fasta.loc.sample apache2_licence.txt apache2_license.txt config.json.sample galaxyaushum.png jbrowse2.py readme.rst static/images/bam.png static/images/bigwig.png static/images/blast.png static/images/opacity.png static/images/sections.png static/images/styling.png static/merlintracksamples.png test-data/all_fasta.loc test-data/index.html test-data/merlin.fa |
| diffstat | 17 files changed, 173 insertions(+), 296 deletions(-) [+] |
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--- a/4f27993eab7751041e8c72047be3ea53_0.bw Fri Jan 19 03:08:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - -<!DOCTYPE HTML> -<html lang="en"> - <!--js-app.mako--> - <head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - - <!-- Set meta description --> - - <meta name="description" content="Log in to Galaxy to get access to more tools and resources. Register now for a free account." /> - - <title> - Galaxy - | ToolFactoryDev - </title> - - <link rel="index" href="/"/> - - <link href="/static/dist/base.css?v=1704404015" media="screen" rel="stylesheet" type="text/css" /> - <link href="/static/style/jquery-ui/smoothness/jquery-ui.css?v=1704404015" media="screen" rel="stylesheet" type="text/css" /> - </head> - - <body scroll="no" class="full-content"> - <!-- Provide mount point for application --> - <main> - <div id="app"></div> - </main> - - - <noscript> - <div class="overlay overlay-background noscript-overlay"> - <div> - <h3 class="title">Javascript Required for Galaxy</h3> - <div> - The Galaxy analysis interface requires a browser with Javascript enabled.<br> - Please enable Javascript and refresh this page. - </div> - </div> - </div> - </noscript> - - - <script src="/static/dist/libs.bundled.js?v=1704404015" type="text/javascript"></script> -<script src="/static/dist/analysis.bundled.js?v=1704404015" type="text/javascript"></script> - - - - <script type="text/javascript"> - console.debug("Initializing javascript application:", "app"); - - // js-app.mako - var options = {"root": "/", "user": {"id": null, "total_disk_usage": 0.0, "nice_total_disk_usage": "0 bytes", "quota_percent": null}, "config": {"enable_notification_system": false, "welcome_directory": "plugins/welcome_page/new_user/static/topics/", "enable_celery_tasks": false, "admin_tool_recommendations_path": "/evol/galaxytf23.1.3/config/tool_recommendations_overwrite.yml", "version_extra": null, "tool_training_recommendations_api_url": "https://training.galaxyproject.org/training-material/api/top-tools.json", "expose_user_email": false, "simplified_workflow_run_ui_job_cache": "off", "toolbox_auto_sort": true, "is_admin_user": false, "message_box_class": "info", "show_welcome_with_login": true, "default_locale": "auto", "visualizations_visible": true, "interactivetools_enable": false, "ga_code": null, "allow_user_creation": false, "enable_account_interface": true, "nginx_upload_path": null, "quota_url": "https://galaxyproject.org/support/account-quotas/", "matomo_site_id": null, "object_store_ids_allowing_selection": [], "wiki_url": "https://galaxyproject.org/", "fixed_delegated_auth": false, "use_remote_user": null, "brand": "ToolFactoryDev", "screencasts_url": "https://www.youtube.com/c/galaxyproject", "helpsite_url": "https://help.galaxyproject.org/", "object_store_allows_id_selection": false, "enable_tool_recommendations": false, "oidc": {}, "plausible_domain": null, "simplified_workflow_run_ui": "prefer", "aws_estimate": false, "user_library_import_dir_available": false, "ftp_upload_site": null, "quota_source_labels": [], "tool_recommendation_model_path": "https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model_v_0.2.hdf5", "enable_quotas": false, "markdown_to_pdf_available": false, "post_user_logout_href": "/root/login?is_logout_redirect=true", "enable_unique_workflow_defaults": false, "enable_oidc": false, "citations_export_message_html": "When writing up your analysis, remember to include all references that should be cited in order to completely describe your work. Also, please remember to <a href=\"https://galaxyproject.org/citing-galaxy\">cite Galaxy<\/a>.", "single_user": false, "python": [3, 10], "enable_beacon_integration": false, "logo_src": "/static/toolfactorylogo.png", "enable_tool_source_display": false, "require_login": true, "datatypes_disable_auto": false, "inactivity_box_content": "Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.", "mailing_join_addr": null, "topk_recommendations": 20, "terms_url": null, "logo_url": "/", "server_startttime": 1704404015, "panel_views": {"default": {"id": "default", "model_class": "type", "name": "Full Tool Panel", "description": "Galaxy's fully configured toolbox panel with all sections, tools, and configured workflows loaded.", "view_type": "default", "searchable": true}, "ontology:edam_operations": {"id": "ontology:edam_operations", "model_class": "EdamToolPanelView", "name": "EDAM Operations", "description": "Tools are grouped using annotated EDAM operation information (if available).", "view_type": "ontology", "searchable": true}, "ontology:edam_topics": {"id": "ontology:edam_topics", "model_class": "EdamToolPanelView", "name": "EDAM Topics", "description": "Tools are grouped using annotated EDAM topic information (if available).", "view_type": "ontology", "searchable": true}}, "message_box_visible": false, "cookie_domain": null, "allow_user_dataset_purge": true, "file_sources_configured": false, "overwrite_model_recommendations": false, "upload_from_form_button": "always-off", "message_box_content": null, "prefer_custos_login": false, "version_minor": "3", "support_url": "https://galaxyproject.org/support/", "registration_warning_message": "Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.", "select_type_workflow_threshold": -1, "release_doc_base_url": "https://docs.galaxyproject.org/en/release_", "plausible_server": null, "lims_doc_url": "https://usegalaxy.org/u/rkchak/p/sts", "tool_training_recommendations_link": "https://training.galaxyproject.org/training-material/by-tool/{training_tool_identifier}.html", "citation_url": "https://galaxyproject.org/citing-galaxy", "matomo_server": null, "chunk_upload_size": 10485760, "welcome_url": "/static/welcome.html", "logo_src_secondary": null, "has_user_tool_filters": true, "remote_user_logout_href": null, "version_major": "23.1", "server_mail_configured": false, "default_panel_view": "default", "tool_training_recommendations": true, "simplified_workflow_run_ui_target_history": "prefer_current", "enable_beta_markdown_export": false, "allow_user_impersonation": false, "themes": {}, "active_view": "analysis", "enable_webhooks": true, "show_inactivity_warning": false, "tool_shed_urls": ["https://toolshed.g2.bx.psu.edu/"], "tool_dynamic_configs": ["/evol/galaxytf23.1.3/local_tools/local_tool_conf.xml"], "stored_workflow_menu_entries": []}, "params": {"redirect": "/datasets/cc4287507a7e4aae/display/4f27993eab7751041e8c72047be3ea53_0.bw"}, "session_csrf_token": "a403b55f14053e4e", "redirect": "/datasets/cc4287507a7e4aae/display/4f27993eab7751041e8c72047be3ea53_0.bw"}; - var bootstrapped = {}; - - config.set({ - options: options, - bootstrapped: bootstrapped, - form_input_auto_focus: false - }); - </script> - - - - <script type="text/javascript"> - - var sentry = {}; - - config.set({ - sentry: sentry - }); - - </script> - - - </body> -</html> - - - - - -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sat Jan 20 07:13:26 2024 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- a/apache2_licence.txt Fri Jan 19 03:08:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,178 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. 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--- a/apache2_license.txt Fri Jan 19 03:08:28 2024 +0000 +++ b/apache2_license.txt Sat Jan 20 07:13:26 2024 +0000 @@ -1,4 +1,5 @@ -Apache License + + Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ @@ -175,27 +176,3 @@ END OF TERMS AND CONDITIONS - APPENDIX: How to apply the Apache License to your work. - - To apply the Apache License to your work, attach the following - boilerplate notice, with the fields enclosed by brackets "{}" - replaced with your own identifying information. (Don't include - the brackets!) The text should be enclosed in the appropriate - comment syntax for the file format. We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright 2023 Dan Vanderkam - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config.json.sample Sat Jan 20 07:13:26 2024 +0000 @@ -0,0 +1,22 @@ +{ + "configuration": { + "rpc": { + "defaultDriver": "WebWorkerRpcDriver", + "drivers": { + "MainThreadRpcDriver": {}, + "WebWorkerRpcDriver": {} + } + }, + "logoPath": { + "locationType": "UriLocation", + "uri": "" + } + }, + "plugins": [], + "assemblies": [], + "tracks": [], + "internetAccounts": [], + "aggregateTextSearchAdapters": [], + "connections": [], + "defaultSession": {} +}
--- a/jbrowse2.py Fri Jan 19 03:08:28 2024 +0000 +++ b/jbrowse2.py Sat Jan 20 07:13:26 2024 +0000 @@ -1147,6 +1147,8 @@ track_types = {} with open(self.config_json_file, "r") as config_file: config_json = json.load(config_file) + if self.config_json: + config_json.update(self.config_json) for track_conf in self.tracksToAdd: track_types[track_conf["trackId"]] = track_conf["type"] @@ -1195,7 +1197,8 @@ ] session_name = data.get("session_name", "New session") - + for key, value in mapped_chars.items(): + session_name = session_name.replace(value, key) # Merge with possibly existing defaultSession (if upgrading a jbrowse instance) session_json = {} if "defaultSession" in config_json: @@ -1209,9 +1212,10 @@ session_json["views"].append(view_json) config_json["defaultSession"] = session_json + self.config_json.update(config_json) with open(self.config_json_file, "w") as config_file: - json.dump(config_json, config_file, indent=2) + json.dump(self.config_json, config_file, indent=2) def add_general_configuration(self, data): """ @@ -1219,11 +1223,13 @@ """ config_path = self.config_json_file - config_json = {} if os.path.exists(config_path): with open(config_path, "r") as config_file: config_json = json.load(config_file) - + else: + config_json = {} + if self.config_json: + config_json.update(self.config_json) config_data = {} config_data["disableAnalytics"] = data.get("analytics", "false") == "true" @@ -1240,9 +1246,9 @@ if not config_json.get("configuration", None): config_json["configuration"] = {} config_json["configuration"].update(config_data) - + self.config_json.update(config_json) with open(config_path, "w") as config_file: - json.dump(config_json, config_file, indent=2) + json.dump(self.config_json, config_file, indent=2) def clone_jbrowse(self): """Clone a JBrowse directory into a destination directory.""" @@ -1424,7 +1430,6 @@ pass track_conf["conf"] = etree_to_dict(track.find("options")) jc.add_general_configuration(general_data) - x = open(args.xml, "r").read() jc.config_json["tracks"] = jc.tracksToAdd jc.write_config() jc.add_default_session(default_session_data)
--- a/readme.rst Fri Jan 19 03:08:28 2024 +0000 +++ b/readme.rst Sat Jan 20 07:13:26 2024 +0000 @@ -30,6 +30,8 @@ will open the preconfigured browser using the default web browser application. +That webserver code is separately under the Apache 2 license copied in this repository. See below for this code's MIT license. + History =======
--- a/test-data/all_fasta.loc Fri Jan 19 03:08:28 2024 +0000 +++ b/test-data/all_fasta.loc Sat Jan 20 07:13:26 2024 +0000 @@ -4,15 +4,16 @@ #all_fasta.loc. This file has the format (white space characters are #TAB characters): # -#<unique_build_id> <dbkey> <display_name> <file_path> +#<unique_build_id> <dbkey> <display_name> <file_path> # #So, all_fasta.loc could look something like this: # -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, #such as with hg19 above. # +merlin merlin Merlin ${__HERE__}/merlin.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.html Sat Jan 20 07:13:26 2024 +0000 @@ -0,0 +1,112 @@ +<!DOCTYPE html> +<html> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> + <title>JBrowse</title> + <link rel="stylesheet" type="text/css" href="css/genome.css"> +</head> +<body> + + <script type="text/javascript"> + // jshint unused: false + var dojoConfig = { + async: true, + baseUrl: './src', + has: { + 'host-node': false // Prevent dojo from being fooled by Electron + } + }; + // Move Electron's require out before loading Dojo + if(window.process&&process.versions&&process.versions.electron) { + window.electronRequire = require; + delete window.require; + } + </script> + <script type="text/javascript" src="src/dojo/dojo.js"></script> + <script type="text/javascript" src="src/JBrowse/init.js"></script> + <script type="text/javascript"> + window.onerror=function(msg){ + if( document.body ) + document.body.setAttribute("JSError",msg); + } + + // puts the main Browser object in this for convenience. feel + // free to move it into function scope if you want to keep it + // out of the global namespace + var JBrowse; + require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ], + function (Browser,ioQuery,JSON) { + // the initial configuration of this JBrowse + // instance + + // NOTE: this initial config is the same as any + // other JBrowse config in any other file. this + // one just sets defaults from URL query params. + // If you are embedding JBrowse in some other app, + // you might as well just set this initial config + // to something like { include: '../my/dynamic/conf.json' }, + // or you could put the entire + // dynamically-generated JBrowse config here. + + // parse the query vars in the page URL + var queryParams = ioQuery.queryToObject( window.location.search.slice(1) ); + + var config = { + containerID: "GenomeBrowser", + + dataRoot: queryParams.data, + queryParams: queryParams, + location: queryParams.loc, + forceTracks: queryParams.tracks, + initialHighlight: queryParams.highlight, + show_nav: queryParams.nav, + show_tracklist: queryParams.tracklist, + show_overview: queryParams.overview, + show_menu: queryParams.menu, + show_tracklabels: queryParams.tracklabels, + highResolutionMode: queryParams.highres, + stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } }, + makeFullViewURL: function( browser ) { + + // the URL for the 'Full view' link + // in embedded mode should be the current + // view URL, except with 'nav', 'tracklist', + // and 'overview' parameters forced to 1. + + return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 }); + }, + updateBrowserURL: true + }; + + //if there is ?addFeatures in the query params, + //define a store for data from the URL + if( queryParams.addFeatures ) { + config.stores.url.features = JSON.parse( queryParams.addFeatures ); + } + + // if there is ?addTracks in the query params, add + // those track configurations to our initial + // configuration + if( queryParams.addTracks ) { + config.tracks = JSON.parse( queryParams.addTracks ); + } + + // if there is ?addStores in the query params, add + // those store configurations to our initial + // configuration + if( queryParams.addStores ) { + config.stores = JSON.parse( queryParams.addStores ); + } + + // create a JBrowse global variable holding the JBrowse instance + JBrowse = new Browser( config ); + }); + </script> + + </head> + + <body> + <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; border: 0;"></div> + <div style="display: none">JBrowseDefaultMainPage</div> + </body> +</html>