diff --git a/jbrowse2/bin/make_tracks_config.pl b/jbrowse2/bin/make_tracks_config.pl index 0120ca49..d0a76e17 100755 --- a/jbrowse2/bin/make_tracks_config.pl +++ b/jbrowse2/bin/make_tracks_config.pl @@ -87,11 +87,16 @@ my $includedir = "$Bin/../config/track_configs"; +my $seenRNASeq = 0; for my $f (@includes) { local $/ = undef; if (!-e "$includedir/$f") { warn "$includedir/$f not found\n"; - next; + next; + } + if ($f =~ "rnaseq_splice") { + next if ($seenRNASeq); + $seenRNASeq++; } open (my $F, "<", "$includedir/$f") or die "$!:$f"; my $data = <$F>; diff --git a/jbrowse2/config/track_configs/c_elegans_PRJNA13758_modencode2_with_peaks.json b/jbrowse2/config/track_configs/c_elegans_PRJNA13758_modencode2_with_peaks.json index 6052f866..d5bb1299 100644 --- a/jbrowse2/config/track_configs/c_elegans_PRJNA13758_modencode2_with_peaks.json +++ b/jbrowse2/config/track_configs/c_elegans_PRJNA13758_modencode2_with_peaks.json @@ -12624,7 +12624,7 @@ } }, { - "name" : "GEI-11 Combined (GFP ChIP), GEI-11_Emb w peaks", + "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_Emb w peaks", "assemblyNames" : [ "c_elegans_PRJNA13758" ], @@ -12653,7 +12653,7 @@ ] }, { - "description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI-11_Emb w peaks", + "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_Emb w peaks", "category" : [ "modENCODE data (2014)", "Transcription Factors", @@ -12673,7 +12673,7 @@ } ], "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks_bigbed_peaks", - "name" : "__GEI-11 Combined (GFP ChIP), GEI-11_Emb peaks", + "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_Emb peaks", "type" : "FeatureTrack", "assemblyNames" : [ "c_elegans_PRJNA13758" @@ -12713,10 +12713,10 @@ "assemblyNames" : [ "c_elegans_PRJNA13758" ], - "name" : "GEI-11 Combined (GFP ChIP), GEI11_L2_GFP w peaks" + "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP w peaks" }, { - "name" : "__GEI-11 Combined (GFP ChIP), GEI11_L2_GFP peaks", + "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP peaks", "assemblyNames" : [ "c_elegans_PRJNA13758" ], @@ -12728,7 +12728,7 @@ }, "type" : "BigBedAdapter" }, - "description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI11_L2_GFP w peaks", + "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L2_GFP w peaks", "displays" : [ { "type" : "LinearBasicDisplay", @@ -12750,7 +12750,7 @@ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_bigbed_peaks" }, { - "name" : "GEI-11 Combined (GFP ChIP), GEI11_L3_GFP w peaks", + "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP w peaks", "type" : "QuantitativeTrack", "assemblyNames" : [ "c_elegans_PRJNA13758" @@ -12779,7 +12779,7 @@ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks" }, { - "description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI11_L3_GFP w peaks", + "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L3_GFP w peaks", "displays" : [ { "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks", @@ -12803,7 +12803,7 @@ "assemblyNames" : [ "c_elegans_PRJNA13758" ], - "name" : "__GEI-11 Combined (GFP ChIP), GEI11_L3_GFP peaks", + "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP peaks", "adapter" : { "bigBedLocation" : { "locationType" : "UriLocation", @@ -12817,7 +12817,7 @@ "assemblyNames" : [ "c_elegans_PRJNA13758" ], - "name" : "GEI-11 Combined (GFP ChIP), GEI11_L4_GFP w peaks", + "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP w peaks", "adapter" : { "bigWigLocation" : { "locationType" : "UriLocation", @@ -12861,7 +12861,7 @@ "Transcription Factors", "GFP ChIP" ], - "description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI11_L4_GFP w peaks", + "description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI11_L4_GFP w peaks", "adapter" : { "type" : "BigBedAdapter", "bigBedLocation" : { @@ -12869,7 +12869,7 @@ "locationType" : "UriLocation" } }, - "name" : "__GEI-11 Combined (GFP ChIP), GEI11_L4_GFP peaks", + "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP peaks", "assemblyNames" : [ "c_elegans_PRJNA13758" ], @@ -12902,14 +12902,14 @@ "c_elegans_PRJNA13758" ], "type" : "QuantitativeTrack", - "name" : "GEI-11 Combined (GFP ChIP), GEI-11_L1 w peaks" + "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_L1 w peaks" }, { "assemblyNames" : [ "c_elegans_PRJNA13758" ], "type" : "FeatureTrack", - "name" : "__GEI-11 Combined (GFP ChIP), GEI-11_L1 peaks", + "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_L1 peaks", "adapter" : { "type" : "BigBedAdapter", "bigBedLocation" : { @@ -12917,7 +12917,7 @@ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/bigbed_binaries/18819_details.gff.bb" } }, - "description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI-11_L1 w peaks", + "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_L1 w peaks", "displays" : [ { "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks", @@ -12954,7 +12954,7 @@ "Transcription Factors", "GFP ChIP" ], - "name" : "GEI-11 Combined (GFP ChIP), GEI-11_YA w peaks", + "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_YA w peaks", "assemblyNames" : [ "c_elegans_PRJNA13758" ], @@ -12972,7 +12972,7 @@ "c_elegans_PRJNA13758" ], "type" : "FeatureTrack", - "name" : "__GEI-11 Combined (GFP ChIP), GEI-11_YA peaks", + "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_YA peaks", "adapter" : { "bigBedLocation" : { "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/bigbed_binaries/18904_details.gff.bb", @@ -12981,7 +12981,7 @@ "type" : "BigBedAdapter" }, "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_bigbed_peaks", - "description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI-11_YA w peaks", + "description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI-11_YA w peaks", "displays" : [ { "type" : "LinearBasicDisplay", @@ -14921,7 +14921,7 @@ } }, { - "name" : "GEI-11 Combined (GFP ChIP) recalled peaks w peaks", + "name" : "SNPC-4 Combined (GFP ChIP) recalled peaks w peaks", "type" : "QuantitativeTrack", "assemblyNames" : [ "c_elegans_PRJNA13758" @@ -14950,7 +14950,7 @@ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_GEI-11 Combined (GFP ChIP) recalled peaks w peaks" }, { - "name" : "__GEI-11 Combined (GFP ChIP) recalled peaks peaks", + "name" : "__SNPC-4 Combined (GFP ChIP) recalled peaks peaks", "assemblyNames" : [ "c_elegans_PRJNA13758" ], @@ -14962,7 +14962,7 @@ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/bigbed_binaries/8063_details.gff.bb" } }, - "description" : "Peak calls for GEI-11 Combined (GFP ChIP) recalled peaks w peaks", + "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP) recalled peaks w peaks", "displays" : [ { "type" : "LinearBasicDisplay",