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Arendt Group
Jbrowse2 Annelids
Commits
f600fccf
Commit
f600fccf
authored
7 months ago
by
Cyril Christophe Daniel Robert Cros
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Let's try with no space in url
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d1ebfd05
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1 merge request
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Merging back to main
Pipeline
#62327
failed
7 months ago
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image/jbrowse_script.sh
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View file @
f600fccf
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@@ -40,15 +40,15 @@ jbrowse add-track https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variant
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN058_vcf.vcf.gz
-a
"pdumv021"
-d
"Tobi's variants"
-n
"SN058"
--category
"Variants"
--trackId
"SN058_vcf"
--indexFile
https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN058_vcf.vcf.gz.tbi
jbrowse add-track https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_EMAPPER.gff.gz
-a
"pmassv1_masked"
-d
"Kevin's GFF file from EMAPPER"
-n
"EMAPPER models"
--category
"Annotation"
--trackId
"emapper-pmass"
--indexFile
https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_EMAPPER.gff.gz.tbi
jbrowse add-track https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz
-a
"pmassv1_masked"
-d
"Kevin's GTF file"
-n
"Gene models"
--category
"Annotation"
--trackId
"annotation-pmass"
--indexFile
https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz.tbi
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN035 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn035"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN054 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn054"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN055 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn055"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN056 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn056"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN057 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn057"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN058 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn058"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/Atlas_Batch1_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 1"
--category
"Tobi BAMs"
--trackId
"variant_atlas_1"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch1_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/Atlas_Batch2_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 2"
--category
"Tobi BAMs"
--trackId
"variant_atlas_2"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch2_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/Atlas_Batch3_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 3"
--category
"Tobi BAMs"
--trackId
"variant_atlas_3"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch3_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/Atlas_Batch4_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 4"
--category
"Tobi BAMs"
--trackId
"variant_atlas_4"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch4_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/Atlas_Batch5_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 5"
--category
"Tobi BAMs"
--trackId
"variant_atlas_5"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch5_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Tobi
BAMs/Atlas_Batch6_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 6"
--category
"Tobi BAMs"
--trackId
"variant_atlas_6"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch6_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN035 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn035"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN054 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn054"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN055 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn055"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN056 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn056"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN057 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn057"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/possorted_genome_bam.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Planetary Biology SN058 Pos sorted"
--category
"Tobi BAMs"
--trackId
"planetary_biol_sn058"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/possorted_genome_bam.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/Atlas_Batch1_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 1"
--category
"Tobi BAMs"
--trackId
"variant_atlas_1"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch1_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/Atlas_Batch2_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 2"
--category
"Tobi BAMs"
--trackId
"variant_atlas_2"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch2_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/Atlas_Batch3_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 3"
--category
"Tobi BAMs"
--trackId
"variant_atlas_3"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch3_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/Atlas_Batch4_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 4"
--category
"Tobi BAMs"
--trackId
"variant_atlas_4"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch4_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/Atlas_Batch5_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 5"
--category
"Tobi BAMs"
--trackId
"variant_atlas_5"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch5_noRG.bam.bai
jbrowse add-track https://s3.embl.de/annelids/pdumv021/TobiBAMs/Atlas_Batch6_noRG.bam
-a
"pdumv021"
-d
"Tobi sends me bam files"
-n
"Variant batches bam no RG 6"
--category
"Tobi BAMs"
--trackId
"variant_atlas_6"
--indexFile
https://s3.embl.de/annelids/pdumv021/Tobi BAMs/Atlas_Batch6_noRG.bam.bai
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