From c52321e30f4674b9105f2c6afdc51c82eae00e67 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Mon, 15 Jul 2024 17:55:37 -0700
Subject: [PATCH 1/2] addresses
 https://github.com/WormBase/website-genome-browsers/issues/260 for jb2 (needs
 a rebuild for 293)

---
 jbrowse2/config/track_configs/genes.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jbrowse2/config/track_configs/genes.json b/jbrowse2/config/track_configs/genes.json
index 4f8b1664..b368bcc2 100644
--- a/jbrowse2/config/track_configs/genes.json
+++ b/jbrowse2/config/track_configs/genes.json
@@ -12,7 +12,7 @@
         "$ASSEMBLY"
       ],
       "formatDetails": {
-         "feature": "jexl:{ curie:null,Alliance:feature.curie?'<a href=\"https://alliancegenome.org/gene/'+feature.curie+'\">'+feature.curie+'</a>':null,JBrowse1: '<a href=\"https://stage.alliancegenome.org/jbrowse/worms/jbrowse-simple/?data=data/$ASSEMBLY' + '&loc=' +feature.refName+':'+feature.start+'..'+feature.end+ '\">'+feature.name+'</a>', WormBase: feature.source=='WormBase'?'<a href=\"https://wormbase.org/get?name='+feature.name+';class=Gene\">Gene Page</a>':''}" 
+         "feature": "jexl:{ curie:null,Alliance:('$ASSEMBLY'!='c_elegans_PRJNA13758')?null:feature.curie?'<a href=\"https://alliancegenome.org/gene/'+feature.curie+'\">'+feature.curie+'</a>':null,JBrowse1: '<a href=\"https://stage.alliancegenome.org/jbrowse/worms/jbrowse-simple/?data=data/$ASSEMBLY' + '&loc=' +feature.refName+':'+feature.start+'..'+feature.end+ '\">'+feature.name+'</a>', WormBase: feature.source=='WormBase'?'<a href=\"https://wormbase.org/get?name='+feature.name+';class=Gene\">Gene Page</a>':''}" 
       },
       "description": "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
       "adapter": {

From 4f80fc0df86ed6365deba74aa24398520c1f54b6 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Wed, 17 Jul 2024 13:36:57 -0700
Subject: [PATCH 2/2] species specific gene config to parallel jb1 config

---
 jbrowse2/config/track_configs/b_malayi_PRJNA10729_genes.json     | 1 +
 jbrowse2/config/track_configs/c_angaria_PRJNA51225_genes.json    | 1 +
 jbrowse2/config/track_configs/c_becei_PRJEB28243_genes.json      | 1 +
 jbrowse2/config/track_configs/c_bovis_PRJEB34497_genes.json      | 1 +
 jbrowse2/config/track_configs/c_brenneri_PRJNA20035_genes.json   | 1 +
 jbrowse2/config/track_configs/c_briggsae_PRJNA10731_genes.json   | 1 +
 jbrowse2/config/track_configs/c_elegans_PRJEB28388_genes.json    | 1 +
 .../{genes.json => c_elegans_PRJNA13758_genes.json}              | 0
 jbrowse2/config/track_configs/c_elegans_PRJNA275000_genes.json   | 1 +
 jbrowse2/config/track_configs/c_inopinata_PRJDB5687_genes.json   | 1 +
 jbrowse2/config/track_configs/c_japonica_PRJNA12591_genes.json   | 1 +
 jbrowse2/config/track_configs/c_latens_PRJNA248912_genes.json    | 1 +
 jbrowse2/config/track_configs/c_nigoni_PRJNA384657_genes.json    | 1 +
 jbrowse2/config/track_configs/c_panamensis_PRJEB28259_genes.json | 1 +
 jbrowse2/config/track_configs/c_parvicauda_PRJEB12595_genes.json | 1 +
 .../config/track_configs/c_quiockensis_PRJEB11354_genes.json     | 1 +
 jbrowse2/config/track_configs/c_remanei_PRJNA53967_genes.json    | 1 +
 jbrowse2/config/track_configs/c_remanei_PRJNA577507_genes.json   | 1 +
 jbrowse2/config/track_configs/c_sinica_PRJNA194557_genes.json    | 1 +
 jbrowse2/config/track_configs/c_sulstoni_PRJEB12601_genes.json   | 1 +
 .../config/track_configs/c_tribulationis_PRJEB12608_genes.json   | 1 +
 jbrowse2/config/track_configs/c_tropicalis_PRJNA53597_genes.json | 1 +
 jbrowse2/config/track_configs/c_uteleia_PRJEB12600_genes.json    | 1 +
 .../config/track_configs/c_waitukubuli_PRJEB12602_genes.json     | 1 +
 jbrowse2/config/track_configs/c_zanzibari_PRJEB12596_genes.json  | 1 +
 jbrowse2/config/track_configs/o_tipulae_PRJEB15512_genes.json    | 1 +
 jbrowse2/config/track_configs/o_volvulus_PRJEB513_genes.json     | 1 +
 jbrowse2/config/track_configs/p_pacificus_PRJNA12644_genes.json  | 1 +
 jbrowse2/config/track_configs/p_redivivus_PRJNA186477_genes.json | 1 +
 jbrowse2/config/track_configs/s_ratti_PRJEB125_genes.json        | 1 +
 jbrowse2/config/track_configs/t_muris_PRJEB126_genes.json        | 1 +
 31 files changed, 30 insertions(+)
 create mode 120000 jbrowse2/config/track_configs/b_malayi_PRJNA10729_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_angaria_PRJNA51225_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_becei_PRJEB28243_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_bovis_PRJEB34497_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_brenneri_PRJNA20035_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_briggsae_PRJNA10731_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_elegans_PRJEB28388_genes.json
 rename jbrowse2/config/track_configs/{genes.json => c_elegans_PRJNA13758_genes.json} (100%)
 create mode 120000 jbrowse2/config/track_configs/c_elegans_PRJNA275000_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_inopinata_PRJDB5687_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_japonica_PRJNA12591_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_latens_PRJNA248912_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_nigoni_PRJNA384657_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_panamensis_PRJEB28259_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_parvicauda_PRJEB12595_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_quiockensis_PRJEB11354_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_remanei_PRJNA53967_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_remanei_PRJNA577507_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_sinica_PRJNA194557_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_sulstoni_PRJEB12601_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_tribulationis_PRJEB12608_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_tropicalis_PRJNA53597_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_uteleia_PRJEB12600_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_waitukubuli_PRJEB12602_genes.json
 create mode 120000 jbrowse2/config/track_configs/c_zanzibari_PRJEB12596_genes.json
 create mode 120000 jbrowse2/config/track_configs/o_tipulae_PRJEB15512_genes.json
 create mode 120000 jbrowse2/config/track_configs/o_volvulus_PRJEB513_genes.json
 create mode 120000 jbrowse2/config/track_configs/p_pacificus_PRJNA12644_genes.json
 create mode 120000 jbrowse2/config/track_configs/p_redivivus_PRJNA186477_genes.json
 create mode 120000 jbrowse2/config/track_configs/s_ratti_PRJEB125_genes.json
 create mode 120000 jbrowse2/config/track_configs/t_muris_PRJEB126_genes.json

diff --git a/jbrowse2/config/track_configs/b_malayi_PRJNA10729_genes.json b/jbrowse2/config/track_configs/b_malayi_PRJNA10729_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/b_malayi_PRJNA10729_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_angaria_PRJNA51225_genes.json b/jbrowse2/config/track_configs/c_angaria_PRJNA51225_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_angaria_PRJNA51225_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_becei_PRJEB28243_genes.json b/jbrowse2/config/track_configs/c_becei_PRJEB28243_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_becei_PRJEB28243_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_bovis_PRJEB34497_genes.json b/jbrowse2/config/track_configs/c_bovis_PRJEB34497_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_bovis_PRJEB34497_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_brenneri_PRJNA20035_genes.json b/jbrowse2/config/track_configs/c_brenneri_PRJNA20035_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_brenneri_PRJNA20035_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_briggsae_PRJNA10731_genes.json b/jbrowse2/config/track_configs/c_briggsae_PRJNA10731_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_briggsae_PRJNA10731_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_elegans_PRJEB28388_genes.json b/jbrowse2/config/track_configs/c_elegans_PRJEB28388_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_elegans_PRJEB28388_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/genes.json b/jbrowse2/config/track_configs/c_elegans_PRJNA13758_genes.json
similarity index 100%
rename from jbrowse2/config/track_configs/genes.json
rename to jbrowse2/config/track_configs/c_elegans_PRJNA13758_genes.json
diff --git a/jbrowse2/config/track_configs/c_elegans_PRJNA275000_genes.json b/jbrowse2/config/track_configs/c_elegans_PRJNA275000_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_elegans_PRJNA275000_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_inopinata_PRJDB5687_genes.json b/jbrowse2/config/track_configs/c_inopinata_PRJDB5687_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_inopinata_PRJDB5687_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_japonica_PRJNA12591_genes.json b/jbrowse2/config/track_configs/c_japonica_PRJNA12591_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_japonica_PRJNA12591_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_latens_PRJNA248912_genes.json b/jbrowse2/config/track_configs/c_latens_PRJNA248912_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_latens_PRJNA248912_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_nigoni_PRJNA384657_genes.json b/jbrowse2/config/track_configs/c_nigoni_PRJNA384657_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_nigoni_PRJNA384657_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_panamensis_PRJEB28259_genes.json b/jbrowse2/config/track_configs/c_panamensis_PRJEB28259_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_panamensis_PRJEB28259_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_parvicauda_PRJEB12595_genes.json b/jbrowse2/config/track_configs/c_parvicauda_PRJEB12595_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_parvicauda_PRJEB12595_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_quiockensis_PRJEB11354_genes.json b/jbrowse2/config/track_configs/c_quiockensis_PRJEB11354_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_quiockensis_PRJEB11354_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_remanei_PRJNA53967_genes.json b/jbrowse2/config/track_configs/c_remanei_PRJNA53967_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_remanei_PRJNA53967_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_remanei_PRJNA577507_genes.json b/jbrowse2/config/track_configs/c_remanei_PRJNA577507_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_remanei_PRJNA577507_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_sinica_PRJNA194557_genes.json b/jbrowse2/config/track_configs/c_sinica_PRJNA194557_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_sinica_PRJNA194557_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_sulstoni_PRJEB12601_genes.json b/jbrowse2/config/track_configs/c_sulstoni_PRJEB12601_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_sulstoni_PRJEB12601_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_tribulationis_PRJEB12608_genes.json b/jbrowse2/config/track_configs/c_tribulationis_PRJEB12608_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_tribulationis_PRJEB12608_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_tropicalis_PRJNA53597_genes.json b/jbrowse2/config/track_configs/c_tropicalis_PRJNA53597_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_tropicalis_PRJNA53597_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_uteleia_PRJEB12600_genes.json b/jbrowse2/config/track_configs/c_uteleia_PRJEB12600_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_uteleia_PRJEB12600_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_waitukubuli_PRJEB12602_genes.json b/jbrowse2/config/track_configs/c_waitukubuli_PRJEB12602_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_waitukubuli_PRJEB12602_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/c_zanzibari_PRJEB12596_genes.json b/jbrowse2/config/track_configs/c_zanzibari_PRJEB12596_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/c_zanzibari_PRJEB12596_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/o_tipulae_PRJEB15512_genes.json b/jbrowse2/config/track_configs/o_tipulae_PRJEB15512_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/o_tipulae_PRJEB15512_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/o_volvulus_PRJEB513_genes.json b/jbrowse2/config/track_configs/o_volvulus_PRJEB513_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/o_volvulus_PRJEB513_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/p_pacificus_PRJNA12644_genes.json b/jbrowse2/config/track_configs/p_pacificus_PRJNA12644_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/p_pacificus_PRJNA12644_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/p_redivivus_PRJNA186477_genes.json b/jbrowse2/config/track_configs/p_redivivus_PRJNA186477_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/p_redivivus_PRJNA186477_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/s_ratti_PRJEB125_genes.json b/jbrowse2/config/track_configs/s_ratti_PRJEB125_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/s_ratti_PRJEB125_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file
diff --git a/jbrowse2/config/track_configs/t_muris_PRJEB126_genes.json b/jbrowse2/config/track_configs/t_muris_PRJEB126_genes.json
new file mode 120000
index 00000000..bf846f6d
--- /dev/null
+++ b/jbrowse2/config/track_configs/t_muris_PRJEB126_genes.json
@@ -0,0 +1 @@
+c_elegans_PRJNA13758_genes.json
\ No newline at end of file