Skip to content
Snippets Groups Projects
Commit f0ac07f2 authored by cyril.cros's avatar cyril.cros
Browse files

Remove EMAPPER

parent ec6f5351
1 merge request!9Reorganized CI
Pipeline #65437 passed
Stage: access_test
    Stage: build_container
      Stage: deploy_to_cluster
        Stage: clean_up_on_failure
          Hide whitespace changes
          Inline Side-by-side
          image/jbrowse_script.sh
          + 0
          − 2
          View file @ f0ac07f2
          ......@@ -15,7 +15,6 @@ jbrowse add-track https://s3.embl.de/annelids/pdumv021/ATACseq/4.final.bigwig -a
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/ATACseq/5.final.bam -a "pdumv021" -d "Lara's Snakemake outputs" -n "Library 5" --category "ATACseq" --trackId "library_bam_5" --indexFile https://s3.embl.de/annelids/pdumv021/ATACseq/5.final.bam.bai
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/ATACseq/5.final.bigwig -a "pdumv021" -d "Lara's Snakemake outputs" -n "Library 5" --category "ATACseq" --trackId "library_bigwig_5" --indexFile https://s3.embl.de/annelids/pdumv021/ATACseq/
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz -a "pdumv021" -d "Kevin's GTF file" -n "Gene models" --category "Annotation" --trackId "annotation" --indexFile https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz.tbi
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_EMAPPER.emapper.gff.gz -a "pdumv021" -d "Kevin's GFF file from EMAPPER" -n "EMAPPER models" --category "Annotation" --trackId "emapper" --indexFile https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_EMAPPER.emapper.gff.gz.tbi
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/MASseq/collapsed.gff.gz -a "pdumv021" -d "MASseq outputs from running isoseq collapse against the Pdum genome" -n "SN073 MASseq isoforms from the 15ng prep" --category "MASseq" --trackId "SN073_15ng_collapsed" --indexFile https://s3.embl.de/annelids/pdumv021/MASseq/collapsed.gff.gz.tbi
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/MASseq/collapsed.gff.gz -a "pdumv021" -d "MASseq outputs from running isoseq collapse against the Pdum genome" -n "SN073 MASseq isoforms" --category "MASseq" --trackId "SN073_60ng_collapsed" --indexFile https://s3.embl.de/annelids/pdumv021/MASseq/collapsed.gff.gz.tbi
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN001_vcf.vcf.gz -a "pdumv021" -d "Tobi's variants" -n "SN001" --category "Variants" --trackId "SN001_vcf" --indexFile https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN001_vcf.vcf.gz.tbi
          ......@@ -38,7 +37,6 @@ jbrowse add-track https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variant
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN056_vcf.vcf.gz -a "pdumv021" -d "Tobi's variants" -n "SN056" --category "Variants" --trackId "SN056_vcf" --indexFile https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN056_vcf.vcf.gz.tbi
          jbrowse add-track https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN057_vcf.vcf.gz -a "pdumv021" -d "Tobi's variants" -n "SN057" --category "Variants" --trackId "SN057_vcf" --indexFile https://s3.embl.de/annelids/pdumv021/Variants/pdumv021_Variants_SN057_vcf.vcf.gz.tbi
          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/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
          ......
          resources_to_s3_NF/tracks.csv
          + 0
          − 2
          View file @ f0ac07f2
          assembly,trackID,name,type,category,description,path,is_text_index
          pmassv1_masked,annotation,Gene models,GTF,Annotation,Kevin's GTF file,/g/arendt/data/platynereis_massiliensis/genes/pmassv1.gtf,TRUE
          pmassv1_masked,emapper,EMAPPER models,GFF,Annotation,Kevin's GFF file from EMAPPER,/g/arendt/data/platynereis_massiliensis/proteome/annotation/pmassv1_EMAPPER.gff,FALSE
          pdumv021,annotation,Gene models,GTF,Annotation,Kevin's GTF file,/g/arendt/data/genome_assemblies/pdum-v2.1/genes/pdumv021.gtf,TRUE
          pdumv021,emapper,EMAPPER models,GFF,Annotation,Kevin's GFF file from EMAPPER,/g/arendt/data/genome_assemblies/pdum-v2.1/proteome/annotation/pdumv021_EMAPPER.emapper.gff,FALSE
          pdumv021,SN035_vcf,SN035,VCF,Variants,Tobi's variants,/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN035.vcf,FALSE
          pdumv021,SN054_vcf,SN054,VCF,Variants,Tobi's variants,/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf,FALSE
          pdumv021,SN055_vcf,SN055,VCF,Variants,Tobi's variants,/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN055.vcf,FALSE
          ......
          0% or .
          You are about to add 0 people to the discussion. Proceed with caution.
          Finish editing this message first!
          Please register or to comment