# HG changeset patch # User fubar # Date 1705734806 0 # Node ID c60b1745629715693b9b873f74d47053f92fe99d # Parent a26c41e304c3fb7bb64a5a74b339beacf9b6662b planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 diff -r a26c41e304c3 -r c60b17456297 4f27993eab7751041e8c72047be3ea53_0.bw --- 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 @@ - - - - - - - - - - - - - Galaxy - | ToolFactoryDev - - - - - - - - - - -
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - diff -r a26c41e304c3 -r c60b17456297 all_fasta.loc.sample --- /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): +# +# +# +#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. +# diff -r a26c41e304c3 -r c60b17456297 apache2_licence.txt --- 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. For the purposes - of this License, Derivative Works shall not include works that remain - separable from, or merely link (or bind by name) to the interfaces of, - the Work and Derivative Works thereof. - - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. - - 2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - copyright license to reproduce, prepare Derivative Works of, - publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. - - 3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - (except as stated in this section) patent license to make, have made, - use, offer to sell, sell, import, and otherwise transfer the Work, - where such license applies only to those patent claims licensable - by such Contributor that are necessarily infringed by their - Contribution(s) alone or by combination of their Contribution(s) - with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. - - 4. Redistribution. You may reproduce and distribute copies of the - Work or Derivative Works thereof in any medium, with or without - modifications, and in Source or Object form, provided that You - meet the following conditions: - - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and - - (b) You must cause any modified files to carry prominent notices - stating that You changed the files; and - - (c) You must retain, in the Source form of any Derivative Works - that You distribute, all copyright, patent, trademark, and - attribution notices from the Source form of the Work, - excluding those notices that do not pertain to any part of - the Derivative Works; and - - (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. - - 5. Submission of Contributions. Unless You explicitly state otherwise, - any Contribution intentionally submitted for inclusion in the Work - by You to the Licensor shall be under the terms and conditions of - this License, without any additional terms or conditions. - Notwithstanding the above, nothing herein shall supersede or modify - the terms of any separate license agreement you may have executed - with Licensor regarding such Contributions. - - 6. Trademarks. This License does not grant permission to use the trade - names, trademarks, service marks, or product names of the Licensor, - except as required for reasonable and customary use in describing the - origin of the Work and reproducing the content of the NOTICE file. - - 7. Disclaimer of Warranty. Unless required by applicable law or - agreed to in writing, Licensor provides the Work (and each - Contributor provides its Contributions) on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or - implied, including, without limitation, any warranties or conditions - of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A - PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any - risks associated with Your exercise of permissions under this License. - - 8. Limitation of Liability. In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - - 9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - END OF TERMS AND CONDITIONS - diff -r a26c41e304c3 -r c60b17456297 apache2_license.txt --- 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. diff -r a26c41e304c3 -r c60b17456297 config.json.sample --- /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": {} +} diff -r a26c41e304c3 -r c60b17456297 galaxyaushum.png Binary file galaxyaushum.png has changed diff -r a26c41e304c3 -r c60b17456297 jbrowse2.py --- 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) diff -r a26c41e304c3 -r c60b17456297 readme.rst --- 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 ======= diff -r a26c41e304c3 -r c60b17456297 static/images/bam.png Binary file static/images/bam.png has changed diff -r a26c41e304c3 -r c60b17456297 static/images/bigwig.png Binary file static/images/bigwig.png has changed diff -r a26c41e304c3 -r c60b17456297 static/images/blast.png Binary file static/images/blast.png has changed diff -r a26c41e304c3 -r c60b17456297 static/images/opacity.png Binary file static/images/opacity.png has changed diff -r a26c41e304c3 -r c60b17456297 static/images/sections.png Binary file static/images/sections.png has changed diff -r a26c41e304c3 -r c60b17456297 static/images/styling.png Binary file static/images/styling.png has changed diff -r a26c41e304c3 -r c60b17456297 static/merlintracksamples.png Binary file static/merlintracksamples.png has changed diff -r a26c41e304c3 -r c60b17456297 test-data/all_fasta.loc --- 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): # -# +# # #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 diff -r a26c41e304c3 -r c60b17456297 test-data/index.html --- /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 @@ + + + + + JBrowse + + + + + + + + + + + + +
+
JBrowseDefaultMainPage
+ + diff -r a26c41e304c3 -r c60b17456297 test-data/merlin.fa