Merge pull request #259 from WormBase/jb2-292

Jb2 292

jbrowse/bin/inline_includes.pl

@@ -115,12 +115,20 @@ =head1 AUTHOR
 my $includedir = "$Bin/../jbrowse/data/c_elegans";
 
 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'}}){

jbrowse/jbrowse/data/c_elegans/includes/simple_rnaseq_splice.json

@@ -1 +1 @@
-rnaseq_splice.json
+c_elegans_PRJNA13758_rnaseq_splice.json

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/
@@ -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/

jbrowse2/bin/make_global_config.pl

@@ -152,10 +152,27 @@
 #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 (undef, undef, $bioproject) = split '_', $assembly;  #literal underscore
+    my @blasttracks = split ",", $tracklist;
+    my $hashref;
+    $$hashref{'bioproject'} = $bioproject;
+    $$hashref{'genomebrowser'}{'tracks'} = \@blasttracks;
+    push @blastarray, $hashref;
+}
+my $toplevelhash;
+$$toplevelhash{'wormbaseVersion'} = 'WS'.$RELEASE;
+$$toplevelhash{'bioprojects'} = \@blastarray;
+print $blastjson JSON->new->pretty(1)->encode($toplevelhash);
+close $blast;
+close $blastjson;
 
 
-
-
-print JSON->new->pretty(1)->encode($json);
-

jbrowse2/bin/make_tracks_config.pl

@@ -53,12 +53,36 @@
 
 #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 = $ASSEMBLY . '_operons.json';
+        # explicitly skip this since the species specific config will get picked up
+        next;
+    }
+    if ($i eq '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/
                             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, $ASSEMBLY . "_protein_motifs";
+    }
+    elsif ($i eq 'variations_classical_alleles.json') {
+        push @blast_tracks, $ASSEMBLY . "_classical_alleles";
+    }
+    elsif ($i eq 'genblastg.json') {
+        push @blast_tracks, $ASSEMBLY . "_genblastg_cds_predictions";
+    }
 }
 
 my $includedir = "$Bin/../config/track_configs";
@@ -92,6 +116,14 @@
 
 #print JSON->new->pretty(1)->encode($outputjson);
 
+open (my $BLAST, ">>", '/blast_tracks.txt') or die "couldn't open blast_tracks.txt: $!";
+
+warn join(',',@blast_tracks);
+if (scalar @blast_tracks > 0) {
+     warn "$ASSEMBLY\t" . join(',',@blast_tracks) . "\n";
+     print $BLAST "$ASSEMBLY\t" . join(',',@blast_tracks) . "\n"; 
+}
+close $BLAST;
 
 # create a 'tracks' section for a server instance
 open (my $trackout, ">", $ASSEMBLY."_tracks.json") or die "$!";