Antismash query

.gitignore

@@ -40,3 +40,4 @@ target
 
 # JBrowse
 /Model/lib/jbrowse/auto_generated/
+.worktrees

Model/lib/jbrowse/aalbSTECLA/tracks.conf

@@ -1,11 +1,8 @@
 [tracks.aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC]
-query.feature=alignment:sequence
-query.edName='aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC'
 category=Gene Models
 key=Anopheles albimanus STECLA build 54 models
-storeClass=JBrowse/Store/SeqFeature/REST
-subParts=block
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AalbimanusSTECLA/alignedTranscripts/gff/aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC/aalbSTECLA_bld54Transcripts_transcript_sequences_RSRC.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
 style.utrColor=grey

Model/lib/jbrowse/acasNeff/tracks.conf

@@ -1,11 +1,8 @@
 [tracks.acasNeff_bld56Transcripts_transcript_sequences_RSRC]
-query.feature=alignment:sequence
-query.edName='acasNeff_bld56Transcripts_transcript_sequences_RSRC'
 category=Gene Models
 key=Transcripts for build 56 models
-storeClass=JBrowse/Store/SeqFeature/REST
-subParts=block
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AcastellaniiNeff/alignedTranscripts/gff/acasNeff_bld56Transcripts_transcript_sequences_RSRC/acasNeff_bld56Transcripts_transcript_sequences_RSRC.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
 style.utrColor=grey

Model/lib/jbrowse/acolNgousso/tracks.conf

@@ -1,11 +1,8 @@
 [tracks.acolNgousso_bld54Transcripts_transcript_sequences_RSRC]
-query.feature=alignment:sequence
-query.edName='acolNgousso_bld54Transcripts_transcript_sequences_RSRC'
 category=Gene Models
 key=Anopheles coluzzii Ngousso build 54 models
-storeClass=JBrowse/Store/SeqFeature/REST
-subParts=block
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AcoluzziiNgousso/alignedTranscripts/gff/acolNgousso_bld54Transcripts_transcript_sequences_RSRC/acolNgousso_bld54Transcripts_transcript_sequences_RSRC.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
 style.utrColor=grey

Model/lib/jbrowse/afumA1163/tracks.conf

@@ -1,12 +1,10 @@
 # [tracks.afumA1163_Weaver_lncRNA_GFF_RSRC]
-# query.feature=gff:basic
-# query.edName='afumA1163_Weaver_lncRNA_GFF_RSRC'
 # category=Gene Models
 # metadata.subcategory=Transcripts
 # metadata.trackType=Segments
-# storeClass=JBrowse/Store/SeqFeature/REST
+# storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+# urlTemplate=/a/service/jbrowse/store?data=AfumigatusA1163/prealigned/gff/afumA1163_Weaver_lncRNA_WebService_RSRC/afumA1163_Weaver_lncRNA.gff.gz
 # style.color={processedTranscriptColor}
-# baseUrl=/a/service/jbrowse
 # type=JBrowse/View/Track/CanvasFeatures
 # glyph=JBrowse/View/FeatureGlyph/Box
 # style.strandArrow=false

Model/lib/jbrowse/afunidAnoFuneDA416_04/tracks.conf

@@ -1,19 +1,22 @@
 
 [tracks.afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_GFF_RSRC]
-query.feature=gff:processedTranscript
-query.edName='afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_GFF_RSRC'
 category=Gene Models
 metadata.subcategory=Transcripts
 metadata.trackType=Processed Transcript
-storeClass=JBrowse/Store/SeqFeature/REST
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AfunestusAfunGA1/prealigned/gff/afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_WebService_RSRC/afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected.gff.gz
+type=NeatCanvasFeatures/View/Track/NeatFeatures
+glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene
+transcriptType={geneTranscriptType}
+noncodingType=nc_transcript
+labelTranscripts=false
+unsafePopup="JSON::true"
 style.color={liftoffTranscriptColor}
 style.borderColor={processedTranscriptBorderColor}
 style.utrColor=grey
-baseUrl=/a/service/jbrowse
-#glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
-type=NeatCanvasFeatures/View/Track/NeatFeatures
+style.topLevelFeaturesPercent=10
+style.labelScale=0.01
 key=Liftoff Gene models of FUMOZ to AfunGA1
-unsafePopup="JSON::true"
 onClick.content={liftoffGeneDetails}
 metadata.dataset=
 fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("afunidAnoFuneDA416_04_FUMOZ_liftoff_phase_corrected_GFF_RSRC", "Liftoff Gene models of FUMOZ to AfunGA1"); }

Model/lib/jbrowse/agamIfakara/tracks.conf

@@ -1,22 +1,24 @@
 [tracks.agamIfakara_GCAv1_to_GCFv2_GFF_RSRC]
-query.feature=gff:processedTranscript
-query.edName='agamIfakara_GCAv1_to_GCFv2_GFF_RSRC'
 category=Gene Models
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
-type=JBrowse/View/Track/CanvasFeatures
-glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
+key=Annotation produced by the Ensembl genebuild
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AgambiaeIfakara/prealigned/gff/agamIfakara_GCAv1_to_GCFv2_WebService_RSRC/agamIfakara_GCAv1_to_GCFv2.gff.gz
+type=NeatCanvasFeatures/View/Track/NeatFeatures
+glyph=NeatCanvasFeatures/View/FeatureGlyph/Gene
+transcriptType={geneTranscriptType}
+noncodingType=nc_transcript
+labelTranscripts=false
+unsafePopup="JSON::true"
 style.color={alternateTranscriptColor}
+style.borderColor={processedTranscriptBorderColor}
 style.utrColor=grey
+style.topLevelFeaturesPercent=10
+style.labelScale=0.01
 onClick.content={gffGeneFeatureTitleFxn}
 menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"}
-key=Annotation produced by the Ensembl genebuild
 metadata.subcategory=Transcripts
 metadata.trackType=Processed Transcript
-metadata.description=${summary}
-fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("${datasetName}", "${datasetDisplayName}"); }
 metadata.description=Annotation produced by the Ensembl genebuild
+fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("${datasetName}", "${datasetDisplayName}"); }
 fmtMetaValue_Description=function() { return datasetDescription("Annotation was produced by the <a href='https://www.ensembl.org/info/genome/genebuild/index.html'>Ensembl genebuild</a>","")}
-onClick.content={DatasetFeatureTitleFxn}
-menuTemplate+=json:{"label": "View Details", "content": "{gffGeneFeatureTitleFxn}"}
 

Model/lib/jbrowse/anidFGSCA4/tracks.conf

@@ -37,20 +37,18 @@ metadata.subcategory=Transcriptional regulatory sites
 metadata.trackType=XYPlot
 
 [tracks.anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC]
-query.feature=alignment:sequence
-query.edName='anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC'
 category=Gene Models
 key=A. nidulans FGSC A4 (2009) Genome Sequence and Annotation
-storeClass=JBrowse/Store/SeqFeature/REST
-subParts=block
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AnidulansFGSCA4/alignedTranscripts/gff/anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC/anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC.gff.gz
+subParts=veupathdb
 type=JBrowse/View/Track/CanvasFeatures
-glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
-style.utrColor=grey
+glyph=JBrowse/View/FeatureGlyph/Segments
 style.color={alternateTranscriptColor}
+style.label=function(feature){ return feature.get("transcriptid"); }
 metadata.subcategory=Transcripts
 metadata.trackType=Processed Transcript
 metadata.dataset=A. nidulans FGSC A4 (2009) Genome Sequence and Annotation
 fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("anidFGSCA4_TurnerAnnotation_transcript_sequences_RSRC", "A. nidulans FGSC A4 (2009) Genome Sequence and Annotation"); }
 menuTemplate+=json:{"label": "View Details", "content": "{sequenceTitleFxn}"}
-onClick.content={sequenceTitleFxn}
+onClick.content=function(track, feature){ var c = track.browser.config; return c.sequenceTitleFxn(track, feature) }

Model/lib/jbrowse/aquaSANGWE/tracks.conf

@@ -1,11 +1,8 @@
 [tracks.aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC]
-query.feature=alignment:sequence
-query.edName='aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC'
 category=Gene Models
 key=Anopheles quadriannulatus SANGWE build 54 models
-storeClass=JBrowse/Store/SeqFeature/REST
-subParts=block
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=AquadriannulatusSANGWE/alignedTranscripts/gff/aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC/aquaSANGWE_bld54Transcripts_transcript_sequences_RSRC.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
 style.utrColor=grey

Model/lib/jbrowse/cimmRS/tracks.conf

@@ -1,8 +1,6 @@
 [tracks.cimmRSKirklandTE]
-query.feature=gff:basic
-query.edName='cimmRS_Kirkland_TE_GFF_RSRC'
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=CimmitisRS/prealigned/gff/cimmRS_Kirkland_TE_WebService_RSRC/cimmRS_Kirkland_TE.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/Box
 key=C. immitis RS TE (Kirkland et al)

Model/lib/jbrowse/cposC735deltSOWgp/tracks.conf

@@ -1,8 +1,6 @@
 [tracks.CposC735KirklandTE]
-query.feature=gff:basic
-query.edName='cposC735deltSOWgp_Kirkland_TE_GFF_RSRC'
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=CposadasiiC735deltSOWgp/prealigned/gff/cposC735deltSOWgp_Kirkland_TE_WebService_RSRC/cposC735deltSOWgp_Kirkland_TE.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/Box
 key=C. posadasii C735 TE (Kirkland et al)

Model/lib/jbrowse/cquiJHB/tracks.conf

@@ -1,11 +1,8 @@
 [tracks.cquiJHB_bld65Transcripts_transcript_sequences_RSRC]
-query.feature=alignment:sequence
-query.edName='cquiJHB_bld65Transcripts_transcript_sequences_RSRC'
 category=Gene Models
 key=Culex quinquefasciatus JHB 2020 transcripts from build 65 models
-storeClass=JBrowse/Store/SeqFeature/REST
-subParts=block
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=CquinquefasciatusJHB2020/alignedTranscripts/gff/cquiJHB_bld65Transcripts_transcript_sequences_RSRC/cquiJHB_bld65Transcripts_transcript_sequences_RSRC.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/ProcessedTranscript
 style.utrColor=grey

Model/lib/jbrowse/edisSAW760/tracks.conf

@@ -1,15 +1,13 @@
 [tracks.edisSAW760_TSS]
-query.feature=gff:basic
-query.edName='edisSAW760_TSS_Mornico_GFF_RSRC'
 category=Sequence Analysis
 metadata.subcategory=Sequence sites, features and motifs
 key=TSS Sites
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=EdisparSAW760/prealigned/gff/edisSAW760_TSS_Mornico_WebService_RSRC/edisSAW760_TSS_Mornico.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/Box
 metadata.dataset=Transcription start sites for E. dispar
-fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("edisSAW760_TSS_Mornico_GFF_RSRC", "Transcription start sites for E. dispar"); }
+fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("edisSAW760_TSS_Mornico_WebService_RSRC", "Transcription start sites for E. dispar"); }
 style.color=black
 style.strandArrow=false
 metadata.trackType=Segments

Model/lib/jbrowse/ehisHM1IMSS/tracks.conf

@@ -20,13 +20,11 @@ region_feature_densities=true
 
 
 [tracks.ehisHM1IMSS_TSS]
-query.feature=gff:basic
-query.edName='ehisHM1IMSS_TSS_Mornico_GFF_RSRC'
 category=Sequence Analysis
 metadata.subcategory=Sequence sites, features and motifs
 key=TSS Sites
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=EhistolyticaHM1IMSS/prealigned/gff/ehisHM1IMSS_TSS_Mornico_WebService_RSRC/ehisHM1IMSS_TSS_Mornico.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/Box
 metadata.dataset=Transcription start sites for E. histolytica

Model/lib/jbrowse/einvIP1/tracks.conf

@@ -1,11 +1,9 @@
 [tracks.einvIP1_TSS]
-query.feature=gff:basic
-query.edName='einvIP1_TSS_Mornico_GFF_RSRC'
 category=Sequence Analysis
 metadata.subcategory=Sequence sites, features and motifs
 key=TSS Sites
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=EinvadensIP1/prealigned/gff/einvIP1_TSS_Mornico_WebService_RSRC/einvIP1_TSS_Mornico.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/Box
 metadata.dataset=Transcription start sites for E. invadens

Model/lib/jbrowse/emosLaredo/tracks.conf

@@ -1,15 +1,13 @@
 [tracks.emosLaredo_TSS]
-query.feature=gff:basic
-query.edName='emosLaredo_TSS_Mornico_GFF_RSRC'
 category=Sequence Analysis
 metadata.subcategory=Sequence sites, features and motifs
 key=TSS Sites
-storeClass=JBrowse/Store/SeqFeature/REST
-baseUrl=/a/service/jbrowse
+storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
+urlTemplate=/a/service/jbrowse/store?data=EmoshkovskiiLaredo/prealigned/gff/emosLaredo_TSS_Mornico_WebService_RSRC/emosLaredo_TSS_Mornico.gff.gz
 type=JBrowse/View/Track/CanvasFeatures
 glyph=JBrowse/View/FeatureGlyph/Box
 metadata.dataset=Transcription start sites for E. moshkovskii
-fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("emosLaredo_TSS_Mornico_GFF_RSRC", "Transcription start sites for E. moshkovskii"); }
+fmtMetaValue_Dataset=function() { return datasetLinkByDatasetName("emosLaredo_TSS_Mornico_WebService_RSRC", "Transcription start sites for E. moshkovskii"); }
 style.color=black
 style.strandArrow=false
 metadata.trackType=Segments