Mercurial > repos > wolma > data_manager_packaged_annotation_data

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"planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91-dirty"
author wolma
date Mon, 20 Dec 2021 10:48:04 +0000
parents 632d33df6758
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632d33df6758 "planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"
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1 #This file describes genome annotation data packages and their contents
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2 #available on the server.
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3 #Such data can consist of any number of individual files in a variety of
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4 #formats (e.g., bed, vcf, tabular) describing any features with respect to the
632d33df6758 "planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"
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5 #genome with the associated dbkey.
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6 #The directory referenced in the <path> column of the table is expected to
632d33df6758 "planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"
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7 #contain the file listed under <data_id> and a meta.yml file with details about
632d33df6758 "planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"
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8 #the annotation package volume and all of its contents.
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9 #This data table has the format (white space characters are TAB characters):
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10 #
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11 #<value> <dbkey> <data_name> <data_id> <data_format> <package_id> <package_name> <path>
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12 #
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13 #So, packaged_annotation_data.loc tables could look like this:
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14 #
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15 #dbSNP_hg19__1__1:dbSNP.tidy hg19 dbSNP tidy (b147.20160601, hg19; from dbSNP/vol:1/build:1) dbSNP.tidy vcf_bgzip dbSNP__hg19__1__1 dbSNP (hg19, vol:1/build:1) /path/to/packaged_annotation_data/hg19/dbSNP/1/1
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16 #Cancer_variant_data__1__1:hotspots.data hg19 CancerHotspots (v2, hg19; from Cancer variant data/vol:1/build:1) hotspots.data bed Cancer_variant_data__hg19__1__1 Cancer variant data (hg19, vol:1/build:1) /path/to/packaged_annotation_data/hg19/Cancer_variant_data/1/1
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17 #Cancer_genes_data__1__1:civic.genes hg19 CIViC genes (01-Feb-2019, hg19; from Cancer gene data/vol:1/build:1) civic.genes tabular Cancer_gene_data__hg19__1__1 Cancer gene data (hg19, vol:1/build:1) /path/to/packaged_annotation_data/hg19/Cancer_variant_data/1/1
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18 #SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1:ARTICv3 NC_045512.2 ARTIC (v3, NC_045512.2; from SARS-CoV-2 amplicon primer sets/vol:1/build:1) ARTICv3 bed6 SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1 SARS-CoV-2 amplicon primer sets (NC_045512.2, vol:1/build:1) /path/to/packaged_annotation_data/NC_045512.2/SARS-CoV-2_amplicon_primer_sets/1/1
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19 #SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1:ARTICv4 NC_045512.2 ARTIC (v4, NC_045512.2; from SARS-CoV-2 amplicon primer sets/vol:1/build:1) ARTICv4 bed6 SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1 SARS-CoV-2 amplicon primer sets (NC_045512.2, vol:1/build:1) /path/to/packaged_annotation_data/NC_045512.2/SARS-CoV-2_amplicon_primer_sets/1/1
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20 #