Add JBrowse2

tools/jbrowse2/.shed.yml

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+name: jbrowse2
+owner: iuc
+categories:
+- Sequence Analysis
+description: JBrowse2 Genome Browser integrated as a Galaxy Tool
+homepage_url: https://jbrowse.org
+long_description: |
+  JBrowse2 is a fast, extensible JS+HTML5 genome browser.
+
+  This repository contains a couple of tools aimed at building up a complete
+  JBrowse2 Genome Browser deployment from raw data files such as gff3, bed, bam,
+  vcf, blastxml, and more...
+
+  The tools produce a ready-to-deploy HTML file and associated processed
+  datasets, allowing visualization of the genome either from within Galaxy, or
+  outside of Galaxy.
+
+  The tool must be allowlisted for HTML content. If BAM files are displayed, it
+  must be served from an proper webserever (e.g. apache or nginx) implementing
+  range requests, though sendfile is optimal.
+
+  https://jbrowse.org
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2
+type: unrestricted

tools/jbrowse2/all_fasta.loc.sample

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+#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.
+#

tools/jbrowse2/apache2_license.txt

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