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Commit 78555646 authored by Cyril Christophe Daniel Robert Cros's avatar Cyril Christophe Daniel Robert Cros
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other space in url removed

parent f600fccf
1 merge request!8Merging back to main
Pipeline #62328 passed
Stage: access_test
    Stage: build_container
      Stage: deploy_to_cluster
        Stage: clean_up_on_failure
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          image/jbrowse_script.sh
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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/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
          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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/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/TobiBAMs/Atlas_Batch6_noRG.bam.bai
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