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author | Ricardo Wurmus <rekado@elephly.net> | 2022-04-14 13:37:23 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-04-14 13:37:23 +0200 |
commit | 03009f2a2bb5c94e94735d2ff9314502412066a4 (patch) | |
tree | f1a0ce4a11d266eea2a23cabd16525147fe78dd6 /gnu/packages/bioconductor.scm | |
parent | c8a6e4abbc4f279f919017d238576cf8724e9456 (diff) | |
download | guix-03009f2a2bb5c94e94735d2ff9314502412066a4.tar.gz |
gnu: r-snplocs-hsapiens-dbsnp144-grch37: Move to annotation section.
* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): Move this variable up to the annotation section.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r-- | gnu/packages/bioconductor.scm | 76 |
1 files changed, 38 insertions, 38 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f795b6ad9c..094bd0d907 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -775,6 +775,44 @@ Ensembl.") Ensembl.") (license license:artistic2.0))) +(define-public r-snplocs-hsapiens-dbsnp144-grch37 + (package + (name "r-snplocs-hsapiens-dbsnp144-grch37") + (version "0.99.20") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" + version 'annotation)) + (sha256 + (base32 + "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + (list r-biocgenerics + r-s4vectors + r-iranges + r-genomeinfodb + r-genomicranges + r-bsgenome + r-biostrings)) + (home-page + "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") + (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") + (description "This package provides SNP locations and alleles for Homo +sapiens extracted from NCBI dbSNP Build 144. The source data files used for +this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped +to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a +patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, +X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for +the mitochondrion chromosome. Therefore, the SNPs in this package can be +injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the +correct position but this injection will exclude chrM (i.e. nothing will be +injected in that sequence).") + (license license:artistic2.0))) + (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene (package (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") @@ -11271,44 +11309,6 @@ and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) -(define-public r-snplocs-hsapiens-dbsnp144-grch37 - (package - (name "r-snplocs-hsapiens-dbsnp144-grch37") - (version "0.99.20") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" - version 'annotation)) - (sha256 - (base32 - "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - (list r-biocgenerics - r-s4vectors - r-iranges - r-genomeinfodb - r-genomicranges - r-bsgenome - r-biostrings)) - (home-page - "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") - (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") - (description "This package provides SNP locations and alleles for Homo -sapiens extracted from NCBI dbSNP Build 144. The source data files used for -this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped -to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a -patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, -X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for -the mitochondrion chromosome. Therefore, the SNPs in this package can be -injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the -correct position but this injection will exclude chrM (i.e. nothing will be -injected in that sequence).") - (license license:artistic2.0))) - (define-public r-reqon (package (name "r-reqon") |