Difference between revisions of "PAG2024 bash script"
From GMOD
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#!/bin/bash | #!/bin/bash | ||
− | jbrowse create public_html --force | + | jbrowse create public_html --force --branch metadata_facet_filters |
cd public_html | cd public_html | ||
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--load inPlace \ | --load inPlace \ | ||
--config '{ "metadata": { "source":"GFF3 created by Scott Cain, from WormBase annotation file at https://downloads.wormbase.org/releases/WS286/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS286.annotations.gff3.gz" } }' | --config '{ "metadata": { "source":"GFF3 created by Scott Cain, from WormBase annotation file at https://downloads.wormbase.org/releases/WS286/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS286.annotations.gff3.gz" } }' | ||
− | + | ||
jbrowse text-index --attributes=Name,ID,locus --tracks c_elegans.genes.sorted.gff3 | jbrowse text-index --attributes=Name,ID,locus --tracks c_elegans.genes.sorted.gff3 | ||
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− | jbrowse add-track https://s3.amazonaws.com/ | + | jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/CeNDR/CB4854.bam \ |
--name "CeNDR BAM" \ | --name "CeNDR BAM" \ | ||
--config '{ "metadata": { "source":"Used by permission from http://elegansvariation.org/" } }' | --config '{ "metadata": { "source":"Used by permission from http://elegansvariation.org/" } }' | ||
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--name c_briggsae_PRJNA10731 \ | --name c_briggsae_PRJNA10731 \ | ||
--type bgzipFasta \ | --type bgzipFasta \ | ||
− | --load inPlace | + | --load inPlace |
jbrowse make-pif data/c_elegans.c_briggsae.paf | jbrowse make-pif data/c_elegans.c_briggsae.paf | ||
− | jbrowse add-track | + | jbrowse add-track c_elegans.c_briggsae.pif.gz \ |
--assemblyNames c_briggsae_PRJNA10731,c_elegans_PRJNA13758 \ | --assemblyNames c_briggsae_PRJNA10731,c_elegans_PRJNA13758 \ | ||
--description "A minimap2 comparison of C. elegans and C. briggsae" \ | --description "A minimap2 comparison of C. elegans and C. briggsae" \ | ||
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--name "C. elegans/C. briggsae Synteny" \ | --name "C. elegans/C. briggsae Synteny" \ | ||
--config '{ "metadata": { "source":"Comparative analysis using this command: minimap2 -c data/c_elegans.PRJNA13758.WS286.genomic.fa.gz data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz > c_elegans.c_briggsae.paf" } }' | --config '{ "metadata": { "source":"Comparative analysis using this command: minimap2 -c data/c_elegans.PRJNA13758.WS286.genomic.fa.gz data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz > c_elegans.c_briggsae.paf" } }' | ||
− | + | ||
jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS287/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz \ | jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS287/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz \ | ||
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--trackId c_briggsae_genes \ | --trackId c_briggsae_genes \ | ||
--config '{ "metadata": { "source":"Curated genes track directly from the WormBase JBrowse 1 instance." } }' | --config '{ "metadata": { "source":"Curated genes track directly from the WormBase JBrowse 1 instance." } }' | ||
− | + | ||
− | jbrowse add-track https://s3.amazonaws.com/ | + | jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/maroilley/candidateSV.vcf.gz \ |
--name "Structural Variant Candidates VCF" \ | --name "Structural Variant Candidates VCF" \ | ||
--assemblyNames c_elegans_PRJNA13758 \ | --assemblyNames c_elegans_PRJNA13758 \ | ||
--category "Structural Variants" | --category "Structural Variants" | ||
− | jbrowse add-track https://s3.amazonaws.com/ | + | jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/maroilley/VC109_Het_trim_bwaMEM_sort.bam \ |
--name "VC109 BAM" \ | --name "VC109 BAM" \ | ||
--assemblyNames c_elegans_PRJNA13758 \ | --assemblyNames c_elegans_PRJNA13758 \ | ||
--category "Structural Variants" | --category "Structural Variants" | ||
</pre> | </pre> |
Revision as of 22:00, 22 December 2023
#!/bin/bash jbrowse create public_html --force --branch metadata_facet_filters cd public_html jbrowse add-assembly data/c_elegans.PRJNA13758.WS286.genomic.fa.gz \ --displayName "C. elegans N2" \ --name c_elegans_PRJNA13758 \ --type bgzipFasta \ --load inPlace \ --refNameAliases data/ce_aliases.txt jbrowse add-track data/c_elegans.genes.sorted.gff3.gz \ --name Genes \ --description "Curated genes from WormBase" \ --load inPlace \ --config '{ "metadata": { "source":"GFF3 created by Scott Cain, from WormBase annotation file at https://downloads.wormbase.org/releases/WS286/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS286.annotations.gff3.gz" } }' jbrowse text-index --attributes=Name,ID,locus --tracks c_elegans.genes.sorted.gff3 jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS286/c_elegans_PRJNA13758/tracks/Curated%20Genes%20\(protein%20coding\)/{refseq}/trackData.jsonz \ --name "Protein coding genes" \ --description "Only protein coding genes from WormBase" \ --config '{ "metadata": { "source":"Directly from WormBases JBrowse 1 instance at https://wormbase.org/tools/genome/jbrowse" } }' jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/CeNDR/CB4854.bam \ --name "CeNDR BAM" \ --config '{ "metadata": { "source":"Used by permission from http://elegansvariation.org/" } }' jbrowse add-track https://storage.googleapis.com/elegansvariation.org/releases/current/WI.current.soft-filtered.vcf.gz \ --name Variants \ --config '{ "metadata": { "source":"Used by permission from http://elegansvariation.org/" } }' jbrowse add-track https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw \ --name "Frame 1 usage" \ --config '{ "metadata": { "source":"Publicly available data from the Broad Institute: https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/mm39/PhyloCSF_raw.html" } }' jbrowse add-track-json '{"type":"MultiQuantitativeTrack","trackId":"multiwiggle_phylo","name":"Forward PhyloCSF","assemblyNames":["c_elegans_PRJNA13758"],"adapter":{"type":"MultiWiggleAdapter","bigWigs":["https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw","https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+2.bw","https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+3.bw"]},"metadata":{"source":"Publicly available data from the Broad Institute: https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/mm39/PhyloCSF_raw.html"},"displays":[{"type":"MultiLinearWiggleDisplay","displayId":"multiwiggle_phylo-MultiLinearWiggleDisplay"}]}' jbrowse add-assembly data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz \ --displayName "C. briggsae" \ --name c_briggsae_PRJNA10731 \ --type bgzipFasta \ --load inPlace jbrowse make-pif data/c_elegans.c_briggsae.paf jbrowse add-track c_elegans.c_briggsae.pif.gz \ --assemblyNames c_briggsae_PRJNA10731,c_elegans_PRJNA13758 \ --description "A minimap2 comparison of C. elegans and C. briggsae" \ --load inPlace \ --name "C. elegans/C. briggsae Synteny" \ --config '{ "metadata": { "source":"Comparative analysis using this command: minimap2 -c data/c_elegans.PRJNA13758.WS286.genomic.fa.gz data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz > c_elegans.c_briggsae.paf" } }' jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS287/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz \ --assemblyNames c_briggsae_PRJNA10731 \ --name "C. briggsae Genes" \ --trackId c_briggsae_genes \ --config '{ "metadata": { "source":"Curated genes track directly from the WormBase JBrowse 1 instance." } }' jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/maroilley/candidateSV.vcf.gz \ --name "Structural Variant Candidates VCF" \ --assemblyNames c_elegans_PRJNA13758 \ --category "Structural Variants" jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/maroilley/VC109_Het_trim_bwaMEM_sort.bam \ --name "VC109 BAM" \ --assemblyNames c_elegans_PRJNA13758 \ --category "Structural Variants"