From 023711e1e46335e67e90b7eafd2844391c750155 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Fri, 8 Mar 2024 10:03:01 -0800
Subject: [PATCH 01/15] trying to fix the splice junction skipping for elegans

---
 jbrowse/bin/inline_includes.pl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/jbrowse/bin/inline_includes.pl b/jbrowse/bin/inline_includes.pl
index 17b59672..bfa15db6 100755
--- a/jbrowse/bin/inline_includes.pl
+++ b/jbrowse/bin/inline_includes.pl
@@ -115,6 +115,9 @@ =head1 AUTHOR
 my $includedir = "$Bin/../jbrowse/data/c_elegans";
 
 for my $f (@includes) {
+    if ($f == 'rnaseq_splice.json') {
+         $f = $BIOPROJECT .'_rnaseq_splice.json';
+    }
     local $/ = undef;
     open (my $F, "<", "$includedir/$f") or die "$!:$f";
     my $data = <$F>;

From b1addd1f04602b6ffc28e6310d0920626858e1e9 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Fri, 8 Mar 2024 14:10:13 -0800
Subject: [PATCH 02/15] getting a little more specific with the splice fix

---
 jbrowse/bin/inline_includes.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jbrowse/bin/inline_includes.pl b/jbrowse/bin/inline_includes.pl
index bfa15db6..7c8ccdc1 100755
--- a/jbrowse/bin/inline_includes.pl
+++ b/jbrowse/bin/inline_includes.pl
@@ -115,8 +115,8 @@ =head1 AUTHOR
 my $includedir = "$Bin/../jbrowse/data/c_elegans";
 
 for my $f (@includes) {
-    if ($f == 'rnaseq_splice.json') {
-         $f = $BIOPROJECT .'_rnaseq_splice.json';
+    if ($f eq 'includes/rnaseq_splice.json') {
+         $f = 'includes/' . $BIOPROJECT .'_rnaseq_splice.json';
     }
     local $/ = undef;
     open (my $F, "<", "$includedir/$f") or die "$!:$f";

From 6d88815aa3810d476fb033d9ea1b1c66c1841210 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sat, 9 Mar 2024 07:06:28 -0800
Subject: [PATCH 03/15] handling the species specific operon config too

---
 jbrowse/bin/inline_includes.pl | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/jbrowse/bin/inline_includes.pl b/jbrowse/bin/inline_includes.pl
index 7c8ccdc1..93f4b5e0 100755
--- a/jbrowse/bin/inline_includes.pl
+++ b/jbrowse/bin/inline_includes.pl
@@ -117,13 +117,18 @@ =head1 AUTHOR
 for my $f (@includes) {
     if ($f eq 'includes/rnaseq_splice.json') {
          $f = 'includes/' . $BIOPROJECT .'_rnaseq_splice.json';
+         warn $f;
+    }
+    if ($f eq 'includes/operons.json') {
+         $f = 'includes/' .$BIOPROJECT .'_operons.json';
+         warn $f;
     }
     local $/ = undef;
     open (my $F, "<", "$includedir/$f") or die "$!:$f";
     my $data = <$F>;
     close $F;
 
-    warn $f;
+    #warn $f;
     $json = JSON->new->decode($data);
 
     for my $a (@{$$json{'tracks'}}){

From 24739ca240f3978c0dada726719fa842b50506e2 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sat, 9 Mar 2024 07:29:34 -0800
Subject: [PATCH 04/15] two changes: creating blast track list and dealing with
 species specific splice and operons

---
 jbrowse2/bin/make_global_config.pl | 22 ++++++++++++++++++----
 jbrowse2/bin/make_tracks_config.pl | 25 +++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 4 deletions(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index b311c742..30a71b17 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -152,10 +152,24 @@
 #I dont think we need several of the things that are empty arrays 
 #in the existing config
 
+print JSON->new->pretty(1)->encode($json);
 
+# build the bioproject-->tracks for jbrowse blast file
+open (my $blast, "<", "blast_tracks.txt") or die "unable to open blast/tracks text file: $!";
+open (my $blastjson, ">", "blast_tracks.json") or die "unable to open blast_tracks.json for writing: $!";
+my @blastarray;
+while (<$blast>) {
+    chomp;
+    my ($assembly, $tracklist) = split /\t/;
+    my ($bioproject) = split '_', $assembly;
+    my @blasttracks = split ",", $tracklist;
+    my $hashref;
+    $$hashref{'bioproject'} = $bioproject;
+    $$hashref{'genomebrowser'}{'tracks'} = @blasttracks;
+    push @blastarray, $hashref;
+}
+print $blastjson JSON->new->pretty(1)->encode(@blastarray);
+close $blast;
+close $blastjson;
 
 
-
-
-print JSON->new->pretty(1)->encode($json);
-
diff --git a/jbrowse2/bin/make_tracks_config.pl b/jbrowse2/bin/make_tracks_config.pl
index c990ff22..d32d0d84 100755
--- a/jbrowse2/bin/make_tracks_config.pl
+++ b/jbrowse2/bin/make_tracks_config.pl
@@ -53,12 +53,32 @@
 
 #create list of track configs to include
 my @includes;
+my @blast_tracks;
 for my $i (@{$$trackList{'include'}}) {
     $i =~ s/includes\///;
+    if ($i eq 'operons.json') {
+        $i = $ASSEMBLY . '_operons.json';
+    }
+    if ($i eq 'rnaseq_splice.json') {
+        $i = $ASSEMBLY . '_rnaseq_splice.json';
+    }
     push @includes, $i unless ($i =~ /functions.conf/
                             or $i =~ /PR.*DNA.json/
                             or $i =~ /alphafold/
                             or $i =~ /expression_patterns/);
+
+    if ($i eq 'genes.json') {
+        push @blast_tracks, $ASSEMBLY . "_curated_genes";
+    }
+    elsif ($i eq 'protein_motifs.json') {
+        push @blast_tracks, $ASSEMBLY . "_protein_motifs";
+    }
+    elsif ($1 eq 'variations_classical_alleles.json') {
+        push @blast_tracks, $ASSEMBLY . "_classical_alleles";
+    }
+    elsif ($1 eq 'genblastg.json') {
+        push @blast_tracks, $ASSEMBLY . "_genblastg_cds_predictions";
+    }
 }
 
 my $includedir = "$Bin/../config/track_configs";
@@ -92,6 +112,11 @@
 
 #print JSON->new->pretty(1)->encode($outputjson);
 
+open (my $BLAST, ">>", 'blast_tracks.txt') or die "couldn't open blast_tracks.txt: $!";
+if (scalar @blast_tracks > 0) {
+     print $BLAST "$ASSEMBLY\t" . join(',',@blast_tracks) . "\n"; 
+}
+close $BLAST;
 
 # create a 'tracks' section for a server instance
 open (my $trackout, ">", $ASSEMBLY."_tracks.json") or die "$!";

From 9e6ee28bb91f3d4e72bed5505c6ee5b5c698ebad Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sat, 9 Mar 2024 11:23:56 -0800
Subject: [PATCH 05/15] renaming the rnaseq_splice conf to make N2 specific

---
 ...aseq_splice.json => c_elegans_PRJNA13758_rnaseq_splice.json} | 0
 .../jbrowse/data/c_elegans/includes/simple_rnaseq_splice.json   | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename jbrowse/jbrowse/data/c_elegans/includes/{rnaseq_splice.json => c_elegans_PRJNA13758_rnaseq_splice.json} (100%)

diff --git a/jbrowse/jbrowse/data/c_elegans/includes/rnaseq_splice.json b/jbrowse/jbrowse/data/c_elegans/includes/c_elegans_PRJNA13758_rnaseq_splice.json
similarity index 100%
rename from jbrowse/jbrowse/data/c_elegans/includes/rnaseq_splice.json
rename to jbrowse/jbrowse/data/c_elegans/includes/c_elegans_PRJNA13758_rnaseq_splice.json
diff --git a/jbrowse/jbrowse/data/c_elegans/includes/simple_rnaseq_splice.json b/jbrowse/jbrowse/data/c_elegans/includes/simple_rnaseq_splice.json
index eca5ea3a..6a567519 120000
--- a/jbrowse/jbrowse/data/c_elegans/includes/simple_rnaseq_splice.json
+++ b/jbrowse/jbrowse/data/c_elegans/includes/simple_rnaseq_splice.json
@@ -1 +1 @@
-rnaseq_splice.json
\ No newline at end of file
+c_elegans_PRJNA13758_rnaseq_splice.json
\ No newline at end of file

From 6eb17d10d7900c3c6b18802b62613c775a87d089 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sun, 10 Mar 2024 07:38:44 -0700
Subject: [PATCH 06/15] fixing the operon and splice config handling. Needs
 testing but should address https://github.com/WormBase/website/issues/9436

---
 jbrowse2/bin/make_tracks_config.pl | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/jbrowse2/bin/make_tracks_config.pl b/jbrowse2/bin/make_tracks_config.pl
index d32d0d84..41ac2618 100755
--- a/jbrowse2/bin/make_tracks_config.pl
+++ b/jbrowse2/bin/make_tracks_config.pl
@@ -57,10 +57,14 @@
 for my $i (@{$$trackList{'include'}}) {
     $i =~ s/includes\///;
     if ($i eq 'operons.json') {
-        $i = $ASSEMBLY . '_operons.json';
+        #$i = $ASSEMBLY . '_operons.json';
+        # explicitly skip this since the species specific config will get picked up
+        next;
     }
     if ($i eq 'rnaseq_splice.json') {
-        $i = $ASSEMBLY . '_rnaseq_splice.json';
+        #$i = $ASSEMBLY . '_rnaseq_splice.json';
+        # explicitly skip this since the species specific config will get picked up
+        next;
     }
     push @includes, $i unless ($i =~ /functions.conf/
                             or $i =~ /PR.*DNA.json/

From 8faef913670843793f88e6ec4c2cac526e5c150a Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sun, 10 Mar 2024 07:46:08 -0700
Subject: [PATCH 07/15] I think the arg for JSON->encode has to be a ref

---
 jbrowse2/bin/make_global_config.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index 30a71b17..e9e40ce0 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -168,7 +168,7 @@
     $$hashref{'genomebrowser'}{'tracks'} = @blasttracks;
     push @blastarray, $hashref;
 }
-print $blastjson JSON->new->pretty(1)->encode(@blastarray);
+print $blastjson JSON->new->pretty(1)->encode(\@blastarray);
 close $blast;
 close $blastjson;
 

From 637de4dc85c9179507a1aa023fe1cddc5b423f4f Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sun, 10 Mar 2024 23:54:29 +0000
Subject: [PATCH 08/15] debugging blast track config build

---
 jbrowse2/Dockerfile.mkzip          | 4 ++--
 jbrowse2/bin/make_tracks_config.pl | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/jbrowse2/Dockerfile.mkzip b/jbrowse2/Dockerfile.mkzip
index 937032f5..5e81c13f 100644
--- a/jbrowse2/Dockerfile.mkzip
+++ b/jbrowse2/Dockerfile.mkzip
@@ -5,11 +5,11 @@
 
 FROM gmod/jbrowse2-buildenv:1.2
 
-ARG RELEASE=289
+ARG RELEASE=292
 ARG AWS_ACCESS_KEY_ID
 ARG AWS_SECRET_ACCESS_KEY
 
-RUN git clone --single-branch --branch jb2-289 https://github.com/WormBase/website-genome-browsers.git
+RUN git clone --single-branch --branch jb2-292 https://github.com/WormBase/website-genome-browsers.git
 
 RUN mkdir -p /usr/share/nginx/html/tools/genome
 WORKDIR /usr/share/nginx/html/tools/genome/
diff --git a/jbrowse2/bin/make_tracks_config.pl b/jbrowse2/bin/make_tracks_config.pl
index 41ac2618..c9a11787 100755
--- a/jbrowse2/bin/make_tracks_config.pl
+++ b/jbrowse2/bin/make_tracks_config.pl
@@ -117,6 +117,8 @@
 #print JSON->new->pretty(1)->encode($outputjson);
 
 open (my $BLAST, ">>", 'blast_tracks.txt') or die "couldn't open blast_tracks.txt: $!";
+
+warn join(',',@blast_tracks);
 if (scalar @blast_tracks > 0) {
      print $BLAST "$ASSEMBLY\t" . join(',',@blast_tracks) . "\n"; 
 }

From 011508f8bb60544793e0fc38175ccb79e8585b45 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Sun, 10 Mar 2024 23:58:04 +0000
Subject: [PATCH 09/15] arg! $i != $1

---
 jbrowse2/bin/make_tracks_config.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jbrowse2/bin/make_tracks_config.pl b/jbrowse2/bin/make_tracks_config.pl
index c9a11787..a18ed91c 100755
--- a/jbrowse2/bin/make_tracks_config.pl
+++ b/jbrowse2/bin/make_tracks_config.pl
@@ -77,10 +77,10 @@
     elsif ($i eq 'protein_motifs.json') {
         push @blast_tracks, $ASSEMBLY . "_protein_motifs";
     }
-    elsif ($1 eq 'variations_classical_alleles.json') {
+    elsif ($i eq 'variations_classical_alleles.json') {
         push @blast_tracks, $ASSEMBLY . "_classical_alleles";
     }
-    elsif ($1 eq 'genblastg.json') {
+    elsif ($i eq 'genblastg.json') {
         push @blast_tracks, $ASSEMBLY . "_genblastg_cds_predictions";
     }
 }

From 2e19473c7a490cdc22f0f1cb86771750258ea3fe Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Mon, 11 Mar 2024 00:08:30 +0000
Subject: [PATCH 10/15] put the blast track config where I can find it (/)

---
 jbrowse2/bin/make_global_config.pl | 4 ++--
 jbrowse2/bin/make_tracks_config.pl | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index e9e40ce0..95cc0717 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -155,8 +155,8 @@
 print JSON->new->pretty(1)->encode($json);
 
 # build the bioproject-->tracks for jbrowse blast file
-open (my $blast, "<", "blast_tracks.txt") or die "unable to open blast/tracks text file: $!";
-open (my $blastjson, ">", "blast_tracks.json") or die "unable to open blast_tracks.json for writing: $!";
+open (my $blast, "<", "/blast_tracks.txt") or die "unable to open blast/tracks text file: $!";
+open (my $blastjson, ">", "/blast_tracks.json") or die "unable to open blast_tracks.json for writing: $!";
 my @blastarray;
 while (<$blast>) {
     chomp;
diff --git a/jbrowse2/bin/make_tracks_config.pl b/jbrowse2/bin/make_tracks_config.pl
index a18ed91c..0120ca49 100755
--- a/jbrowse2/bin/make_tracks_config.pl
+++ b/jbrowse2/bin/make_tracks_config.pl
@@ -116,10 +116,11 @@
 
 #print JSON->new->pretty(1)->encode($outputjson);
 
-open (my $BLAST, ">>", 'blast_tracks.txt') or die "couldn't open blast_tracks.txt: $!";
+open (my $BLAST, ">>", '/blast_tracks.txt') or die "couldn't open blast_tracks.txt: $!";
 
 warn join(',',@blast_tracks);
 if (scalar @blast_tracks > 0) {
+     warn "$ASSEMBLY\t" . join(',',@blast_tracks) . "\n";
      print $BLAST "$ASSEMBLY\t" . join(',',@blast_tracks) . "\n"; 
 }
 close $BLAST;

From bae598d9701c62151d8a73f08dd8563bc3008333 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Mon, 11 Mar 2024 00:40:23 +0000
Subject: [PATCH 11/15] cleaning up blast config output

---
 jbrowse2/bin/make_global_config.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index 95cc0717..ce8c393d 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -165,7 +165,7 @@
     my @blasttracks = split ",", $tracklist;
     my $hashref;
     $$hashref{'bioproject'} = $bioproject;
-    $$hashref{'genomebrowser'}{'tracks'} = @blasttracks;
+    $$hashref{'genomebrowser'}{'tracks'} = \@blasttracks;
     push @blastarray, $hashref;
 }
 print $blastjson JSON->new->pretty(1)->encode(\@blastarray);

From 42bede2b567b5f87528283ab8e0e7a6d3219a56c Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Mon, 11 Mar 2024 00:49:19 +0000
Subject: [PATCH 12/15] fixing the split for bioproject

---
 jbrowse2/bin/make_global_config.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index ce8c393d..4b2b8e7f 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -161,7 +161,7 @@
 while (<$blast>) {
     chomp;
     my ($assembly, $tracklist) = split /\t/;
-    my ($bioproject) = split '_', $assembly;
+    my ($bioproject) = split '\_', $assembly;  #literal underscore
     my @blasttracks = split ",", $tracklist;
     my $hashref;
     $$hashref{'bioproject'} = $bioproject;

From e4ed09b500e5875958f72413f7d8d9326c8f8539 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Mon, 11 Mar 2024 01:00:41 +0000
Subject: [PATCH 13/15] catching the right item of the assembly name

---
 jbrowse2/bin/make_global_config.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index 4b2b8e7f..76f091e6 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -161,7 +161,7 @@
 while (<$blast>) {
     chomp;
     my ($assembly, $tracklist) = split /\t/;
-    my ($bioproject) = split '\_', $assembly;  #literal underscore
+    my (undef, undef, $bioproject) = split '_', $assembly;  #literal underscore
     my @blasttracks = split ",", $tracklist;
     my $hashref;
     $$hashref{'bioproject'} = $bioproject;

From 0b51569d04f93fba52fbc2b169fc766191757381 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Mon, 11 Mar 2024 01:10:45 +0000
Subject: [PATCH 14/15] adding the ability to create the blast_track json file

---
 jbrowse2/Dockerfile.mkzip | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/jbrowse2/Dockerfile.mkzip b/jbrowse2/Dockerfile.mkzip
index 5e81c13f..5e41bc54 100644
--- a/jbrowse2/Dockerfile.mkzip
+++ b/jbrowse2/Dockerfile.mkzip
@@ -49,6 +49,8 @@ RUN ../../../bin/make_embed_config.pl --release $RELEASE
 RUN ../../../bin/make_global_config.pl --release $RELEASE > config.json
 
 RUN cp config.json /usr/share/nginx/html/tools/genome/jbrowse2/config.json
+RUN cp /blast_tracks.json /usr/share/nginx/html/tools/genome/jbrowse2/blast_tracks.json
+RUN cp /blast_tracks.txt /usr/share/nginx/html/tools/genome/jbrowse2/blast_tracks.txt
 
 RUN mkdir -p /usr/share/nginx/html/tools/genome/jbrowse2/embed/
 RUN cp *embed.json /usr/share/nginx/html/tools/genome/jbrowse2/embed/

From 735dcc46eb84026d4a8104639895e9f5eddae6b3 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Thu, 14 Mar 2024 10:52:32 -0700
Subject: [PATCH 15/15] possible change to blast config--needs testing

---
 jbrowse2/bin/make_global_config.pl | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl
index 76f091e6..8b7c7892 100755
--- a/jbrowse2/bin/make_global_config.pl
+++ b/jbrowse2/bin/make_global_config.pl
@@ -168,7 +168,10 @@
     $$hashref{'genomebrowser'}{'tracks'} = \@blasttracks;
     push @blastarray, $hashref;
 }
-print $blastjson JSON->new->pretty(1)->encode(\@blastarray);
+my $toplevelhash;
+$$toplevelhash{'wormbaseVersion'} = 'WS'.$RELEASE;
+$$toplevelhash{'bioprojects'} = \@blastarray;
+print $blastjson JSON->new->pretty(1)->encode($toplevelhash);
 close $blast;
 close $blastjson;