Jbrowse2

tools/jbrowse2/.shed.yml

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+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 whitelisted for HTML content. If BAM files are displayed, it
+  must be served from an apache or nginx server implementing sendfile.
+
+  https://jbrowse.org
+name: jbrowse2
+owner: iuc
+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/blastxml_to_gapped_gff3.py

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+../blastxml_to_gapped_gff3/blastxml_to_gapped_gff3.py

tools/jbrowse2/config.json.sample

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+{
+  "configuration": {
+    "rpc": {
+      "defaultDriver": "WebWorkerRpcDriver",
+      "drivers": {
+        "MainThreadRpcDriver": {},
+        "WebWorkerRpcDriver": {}
+      }
+    },
+    "logoPath": {
+      "locationType": "UriLocation",
+      "uri": ""
+    }
+  },
+  "plugins": [],
+  "assemblies": [],
+  "tracks": [],
+  "internetAccounts": [],
+  "aggregateTextSearchAdapters": [],
+  "connections": [],
+  "defaultSession": {}
+}

tools/jbrowse2/convertMAF.sh

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+#!/usr/bin/env bash
+# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
+#  MAF file must contain the species name and chromosome name
+#  e.g. hg38.chr1 in the sequence identifiers.
+$3/maf2bed.pl $2 < $1 > `basename $1`.bed
+sort -k1,1 -k2,2n `basename $1`.bed > `basename $1`.sorted.bed
+bgzip `basename $1`.sorted.bed
+tabix -p bed `basename $1`.sorted.bed.gz

tools/jbrowse2/gff3_rebase.py

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+../gff3_rebase/gff3_rebase.py