From 3be5667a0c3ec0e8d2e6411e3750d70c06143150 Mon Sep 17 00:00:00 2001
From: GuilhemSempere <guilhem.sempere@cirad.fr>
Date: Mon, 23 Sep 2024 08:47:57 +0200
Subject: [PATCH] Merge from master (#145)

* Update build.yml

* Reverted back to original build.sh

* Added missing file (possibly forgot to commmit/push it) (#136)

* added python build file to get dynamically current pom.xml dependencies, add build.sh deprecated and improve current github workflow (#138)

Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr>

* Update genomes.json

Add 4 new genomes for Citrus medica, C. micrantha, C. maxima and C. reticulata

---------

Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr>
Co-authored-by: droc <gaetan.droc@cirad.fr>
---
 src/main/webapp/res/genomes.json | 70 +++++++++++++++++++++++++++++++-
 1 file changed, 69 insertions(+), 1 deletion(-)

diff --git a/src/main/webapp/res/genomes.json b/src/main/webapp/res/genomes.json
index 5dce990f..8580209c 100644
--- a/src/main/webapp/res/genomes.json
+++ b/src/main/webapp/res/genomes.json
@@ -186,5 +186,73 @@
        "order": 0
      }
     ]
+  },
+  {
+   "id": "citrus_medica",
+   "name": "Citrus medica",
+   "fastaURL": "https://jbrowse.southgreen.fr/citrus_medica/seq/CITME.fasta",
+   "indexURL": "https://jbrowse.southgreen.fr/citrus_medica/seq/CITME.fasta.fai",
+   "tracks": [
+     {
+       "name": "Locus",
+       "type": "annotation",
+       "format": "gff3",
+       "sourceType": "file",
+       "url": "https://jbrowse.southgreen.fr/citrus_medica/gff3/CITME.gff3.gz",
+       "indexURL": "https://jbrowse.southgreen.fr/citrus_medica/gff3/CITME.gff3.gz.tbi",
+       "order": 0
+     }
+    ]
+  },
+  {
+   "id": "citrus_reticulata",
+   "name": "Citrus reticulata",
+   "fastaURL": "https://jbrowse.southgreen.fr/citrus_reticulata/seq/CITRE.fasta",
+   "indexURL": "https://jbrowse.southgreen.fr/citrus_reticulata/seq/CITRE.fasta.fai",
+   "tracks": [
+     {
+       "name": "Locus",
+       "type": "annotation",
+       "format": "gff3",
+       "sourceType": "file",
+       "url": "https://jbrowse.southgreen.fr/citrus_reticulata/gff3/CITRE.gff3.gz",
+       "indexURL": "https://jbrowse.southgreen.fr/citrus_reticulata/gff3/CITRE.gff3.gz.tbi",
+       "order": 0
+     }
+    ]
+  },
+  {
+   "id": "citrus_micrantha",
+   "name": "Citrus micrantha",
+   "fastaURL": "https://jbrowse.southgreen.fr/citrus_micrantha/seq/CITMI.fasta",
+   "indexURL": "https://jbrowse.southgreen.fr/citrus_micrantha/seq/CITMI.fasta.fai",
+   "tracks": [
+     {
+       "name": "Locus",
+       "type": "annotation",
+       "format": "gff3",
+       "sourceType": "file",
+       "url": "https://jbrowse.southgreen.fr/citrus_micrantha/gff3/CITMI.gff3.gz",
+       "indexURL": "https://jbrowse.southgreen.fr/citrus_micrantha/gff3/CITMI.gff3.gz.tbi",
+       "order": 0
+     }
+    ]
+  },
+  {
+   "id": "citrus_maxima",
+   "name": "Citrus maxima",
+   "fastaURL": "https://jbrowse.southgreen.fr/citrus_maxima/seq/CITMA.fasta",
+   "indexURL": "https://jbrowse.southgreen.fr/citrus_maxima/seq/CITMA.fasta.fai",
+   "tracks": [
+     {
+       "name": "Locus",
+       "type": "annotation",
+       "format": "gff3",
+       "sourceType": "file",
+       "url": "https://jbrowse.southgreen.fr/citrus_maxima/gff3/CITMA.gff3.gz",
+       "indexURL": "https://jbrowse.southgreen.fr/citrus_maxima/gff3/CITMA.gff3.gz.tbi",
+       "order": 0
+     }
+    ]
   }
-]
\ No newline at end of file
+]