From c6cde5f5fa55050ad70d5e286e4db618a67773f6 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Fri, 2 Apr 2021 15:42:36 -0400 Subject: [PATCH] Relocate display application configs and include display application configs in galaxy-webapps package. --- .../datatypes/display_applications/configs}/biom/biom_simple.xml | 0 .../display_applications/configs}/ensembl/ensembl_bam.xml | 0 .../display_applications/configs}/ensembl/ensembl_gff.xml | 0 .../configs}/ensembl/ensembl_interval_as_bed.xml | 0 .../display_applications/configs}/gbrowse/gbrowse_gff.xml | 0 .../configs}/gbrowse/gbrowse_interval_as_bed.xml | 0 .../display_applications/configs}/gbrowse/gbrowse_wig.xml | 0 .../display_applications/configs}/icn3d/icn3d_simple.xml | 0 .../galaxy/datatypes/display_applications/configs}/igb/bam.xml | 0 .../galaxy/datatypes/display_applications/configs}/igb/bb.xml | 0 .../galaxy/datatypes/display_applications/configs}/igb/bed.xml | 0 .../datatypes/display_applications/configs}/igb/bedgraph.xml | 0 .../datatypes/display_applications/configs}/igb/bigwig.xml | 0 .../galaxy/datatypes/display_applications/configs}/igb/gtf.xml | 0 .../galaxy/datatypes/display_applications/configs}/igb/wig.xml | 0 .../galaxy/datatypes/display_applications/configs}/igv/bam.xml | 0 .../datatypes/display_applications/configs}/igv/bigwig.xml | 0 .../datatypes/display_applications/configs}/igv/genbank.xml | 0 .../datatypes/display_applications/configs}/igv/genome_fasta.xml | 0 .../galaxy/datatypes/display_applications/configs}/igv/gff.xml | 0 .../display_applications/configs}/igv/interval_as_bed.xml | 0 .../galaxy/datatypes/display_applications/configs}/igv/vcf.xml | 0 .../display_applications/configs}/intermine/intermine_simple.xml | 0 .../galaxy/datatypes/display_applications/configs}/iobio/bam.xml | 0 .../galaxy/datatypes/display_applications/configs}/iobio/vcf.xml | 0 .../datatypes/display_applications/configs}/rviewer/bed.xml | 0 .../datatypes/display_applications/configs}/rviewer/vcf.xml | 0 .../galaxy/datatypes/display_applications/configs}/ucsc/bam.xml | 0 .../datatypes/display_applications/configs}/ucsc/bigbed.xml | 0 .../datatypes/display_applications/configs}/ucsc/bigwig.xml | 0 .../display_applications/configs}/ucsc/interval_as_bed.xml | 0 .../display_applications/configs}/ucsc/maf_customtrack.xml | 0 .../datatypes/display_applications/configs}/ucsc/trackhub.xml | 0 .../galaxy/datatypes/display_applications/configs}/ucsc/vcf.xml | 0 packages/webapps/MANIFEST.in | 1 + packages/webapps/galaxy/datatypes/display_applications/configs | 1 + 36 files changed, 2 insertions(+) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/biom/biom_simple.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ensembl/ensembl_bam.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ensembl/ensembl_gff.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ensembl/ensembl_interval_as_bed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/gbrowse/gbrowse_gff.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/gbrowse/gbrowse_interval_as_bed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/gbrowse/gbrowse_wig.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/icn3d/icn3d_simple.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/bam.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/bb.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/bed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/bedgraph.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/bigwig.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/gtf.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igb/wig.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/bam.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/bigwig.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/genbank.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/genome_fasta.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/gff.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/interval_as_bed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/igv/vcf.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/intermine/intermine_simple.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/iobio/bam.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/iobio/vcf.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/rviewer/bed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/rviewer/vcf.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/bam.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/bigbed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/bigwig.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/interval_as_bed.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/maf_customtrack.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/trackhub.xml (100%) rename {display_applications => lib/galaxy/datatypes/display_applications/configs}/ucsc/vcf.xml (100%) create mode 120000 packages/webapps/galaxy/datatypes/display_applications/configs diff --git a/display_applications/biom/biom_simple.xml b/lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml similarity index 100% rename from display_applications/biom/biom_simple.xml rename to lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml diff --git a/display_applications/ensembl/ensembl_bam.xml b/lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_bam.xml similarity index 100% rename from display_applications/ensembl/ensembl_bam.xml rename to lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_bam.xml diff --git a/display_applications/ensembl/ensembl_gff.xml b/lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_gff.xml similarity index 100% rename from display_applications/ensembl/ensembl_gff.xml rename to lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_gff.xml diff --git a/display_applications/ensembl/ensembl_interval_as_bed.xml b/lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_interval_as_bed.xml similarity index 100% rename from display_applications/ensembl/ensembl_interval_as_bed.xml rename to lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_interval_as_bed.xml diff --git a/display_applications/gbrowse/gbrowse_gff.xml b/lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_gff.xml similarity index 100% rename from display_applications/gbrowse/gbrowse_gff.xml rename to lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_gff.xml diff --git a/display_applications/gbrowse/gbrowse_interval_as_bed.xml b/lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_interval_as_bed.xml similarity index 100% rename from display_applications/gbrowse/gbrowse_interval_as_bed.xml rename to lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_interval_as_bed.xml diff --git a/display_applications/gbrowse/gbrowse_wig.xml b/lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_wig.xml similarity index 100% rename from display_applications/gbrowse/gbrowse_wig.xml rename to lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_wig.xml diff --git a/display_applications/icn3d/icn3d_simple.xml b/lib/galaxy/datatypes/display_applications/configs/icn3d/icn3d_simple.xml similarity index 100% rename from display_applications/icn3d/icn3d_simple.xml rename to lib/galaxy/datatypes/display_applications/configs/icn3d/icn3d_simple.xml diff --git a/display_applications/igb/bam.xml b/lib/galaxy/datatypes/display_applications/configs/igb/bam.xml similarity index 100% rename from display_applications/igb/bam.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/bam.xml diff --git a/display_applications/igb/bb.xml b/lib/galaxy/datatypes/display_applications/configs/igb/bb.xml similarity index 100% rename from display_applications/igb/bb.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/bb.xml diff --git a/display_applications/igb/bed.xml b/lib/galaxy/datatypes/display_applications/configs/igb/bed.xml similarity index 100% rename from display_applications/igb/bed.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/bed.xml diff --git a/display_applications/igb/bedgraph.xml b/lib/galaxy/datatypes/display_applications/configs/igb/bedgraph.xml similarity index 100% rename from display_applications/igb/bedgraph.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/bedgraph.xml diff --git a/display_applications/igb/bigwig.xml b/lib/galaxy/datatypes/display_applications/configs/igb/bigwig.xml similarity index 100% rename from display_applications/igb/bigwig.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/bigwig.xml diff --git a/display_applications/igb/gtf.xml b/lib/galaxy/datatypes/display_applications/configs/igb/gtf.xml similarity index 100% rename from display_applications/igb/gtf.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/gtf.xml diff --git a/display_applications/igb/wig.xml b/lib/galaxy/datatypes/display_applications/configs/igb/wig.xml similarity index 100% rename from display_applications/igb/wig.xml rename to lib/galaxy/datatypes/display_applications/configs/igb/wig.xml diff --git a/display_applications/igv/bam.xml b/lib/galaxy/datatypes/display_applications/configs/igv/bam.xml similarity index 100% rename from display_applications/igv/bam.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/bam.xml diff --git a/display_applications/igv/bigwig.xml b/lib/galaxy/datatypes/display_applications/configs/igv/bigwig.xml similarity index 100% rename from display_applications/igv/bigwig.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/bigwig.xml diff --git a/display_applications/igv/genbank.xml b/lib/galaxy/datatypes/display_applications/configs/igv/genbank.xml similarity index 100% rename from display_applications/igv/genbank.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/genbank.xml diff --git a/display_applications/igv/genome_fasta.xml b/lib/galaxy/datatypes/display_applications/configs/igv/genome_fasta.xml similarity index 100% rename from display_applications/igv/genome_fasta.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/genome_fasta.xml diff --git a/display_applications/igv/gff.xml b/lib/galaxy/datatypes/display_applications/configs/igv/gff.xml similarity index 100% rename from display_applications/igv/gff.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/gff.xml diff --git a/display_applications/igv/interval_as_bed.xml b/lib/galaxy/datatypes/display_applications/configs/igv/interval_as_bed.xml similarity index 100% rename from display_applications/igv/interval_as_bed.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/interval_as_bed.xml diff --git a/display_applications/igv/vcf.xml b/lib/galaxy/datatypes/display_applications/configs/igv/vcf.xml similarity index 100% rename from display_applications/igv/vcf.xml rename to lib/galaxy/datatypes/display_applications/configs/igv/vcf.xml diff --git a/display_applications/intermine/intermine_simple.xml b/lib/galaxy/datatypes/display_applications/configs/intermine/intermine_simple.xml similarity index 100% rename from display_applications/intermine/intermine_simple.xml rename to lib/galaxy/datatypes/display_applications/configs/intermine/intermine_simple.xml diff --git a/display_applications/iobio/bam.xml b/lib/galaxy/datatypes/display_applications/configs/iobio/bam.xml similarity index 100% rename from display_applications/iobio/bam.xml rename to lib/galaxy/datatypes/display_applications/configs/iobio/bam.xml diff --git a/display_applications/iobio/vcf.xml b/lib/galaxy/datatypes/display_applications/configs/iobio/vcf.xml similarity index 100% rename from display_applications/iobio/vcf.xml rename to lib/galaxy/datatypes/display_applications/configs/iobio/vcf.xml diff --git a/display_applications/rviewer/bed.xml b/lib/galaxy/datatypes/display_applications/configs/rviewer/bed.xml similarity index 100% rename from display_applications/rviewer/bed.xml rename to lib/galaxy/datatypes/display_applications/configs/rviewer/bed.xml diff --git a/display_applications/rviewer/vcf.xml b/lib/galaxy/datatypes/display_applications/configs/rviewer/vcf.xml similarity index 100% rename from display_applications/rviewer/vcf.xml rename to lib/galaxy/datatypes/display_applications/configs/rviewer/vcf.xml diff --git a/display_applications/ucsc/bam.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/bam.xml similarity index 100% rename from display_applications/ucsc/bam.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/bam.xml diff --git a/display_applications/ucsc/bigbed.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/bigbed.xml similarity index 100% rename from display_applications/ucsc/bigbed.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/bigbed.xml diff --git a/display_applications/ucsc/bigwig.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/bigwig.xml similarity index 100% rename from display_applications/ucsc/bigwig.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/bigwig.xml diff --git a/display_applications/ucsc/interval_as_bed.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/interval_as_bed.xml similarity index 100% rename from display_applications/ucsc/interval_as_bed.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/interval_as_bed.xml diff --git a/display_applications/ucsc/maf_customtrack.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/maf_customtrack.xml similarity index 100% rename from display_applications/ucsc/maf_customtrack.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/maf_customtrack.xml diff --git a/display_applications/ucsc/trackhub.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/trackhub.xml similarity index 100% rename from display_applications/ucsc/trackhub.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/trackhub.xml diff --git a/display_applications/ucsc/vcf.xml b/lib/galaxy/datatypes/display_applications/configs/ucsc/vcf.xml similarity index 100% rename from display_applications/ucsc/vcf.xml rename to lib/galaxy/datatypes/display_applications/configs/ucsc/vcf.xml diff --git a/packages/webapps/MANIFEST.in b/packages/webapps/MANIFEST.in index 8393a3b8e2a..fcfa3c8f286 100644 --- a/packages/webapps/MANIFEST.in +++ b/packages/webapps/MANIFEST.in @@ -1 +1,2 @@ include *.rst *.txt LICENSE +include galaxy/datatypes/display_applications/configs/*/*.xml diff --git a/packages/webapps/galaxy/datatypes/display_applications/configs b/packages/webapps/galaxy/datatypes/display_applications/configs new file mode 120000 index 00000000000..bd4fe9cae4a --- /dev/null +++ b/packages/webapps/galaxy/datatypes/display_applications/configs @@ -0,0 +1 @@ +../../../../../lib/galaxy/datatypes/display_applications/configs \ No newline at end of file