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-rw-r--r--gnu/packages/bioconductor.scm221
1 files changed, 43 insertions, 178 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 89547be66d..5c191a2c0b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -76,21 +76,14 @@ objects.")
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Celegans.UCSC.ce10_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
+ version 'annotation))
(sha256
(base32
"1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
(properties
`((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -108,21 +101,14 @@ objects.")
(version "1.4.1")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm6_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
+ version 'annotation))
(sha256
(base32
"1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
(properties
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -140,21 +126,14 @@ objects.")
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm3_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
+ version 'annotation))
(sha256
(base32
"19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
(properties
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -172,12 +151,8 @@ Biostrings objects.")
(version "1.3.99")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
+ version 'annotation))
(sha256
(base32
"1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
@@ -207,21 +182,14 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
(version "0.99.1")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.1000genomes.hs37d5_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
+ version 'annotation))
(sha256
(base32
"1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -238,12 +206,8 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
(version "1.3.99")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.UCSC.hg19.masked_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
+ version 'annotation))
(sha256
(base32
"0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
@@ -273,21 +237,14 @@ default.")
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm9_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
+ version 'annotation))
(sha256
(base32
"1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
(properties
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -304,12 +261,8 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
(version "1.3.99")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm9.masked_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
+ version 'annotation))
(sha256
(base32
"00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
@@ -339,21 +292,14 @@ default." )
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm10_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
+ version 'annotation))
(sha256
(base32
"12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
(properties
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -371,11 +317,7 @@ in Biostrings objects.")
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Ce.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
(sha256
(base32
"1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
@@ -397,11 +339,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Dm.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
(sha256
(base32
"1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
@@ -423,11 +361,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Dr.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
(sha256
(base32
"1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
@@ -449,11 +383,7 @@ based on mapping using Entrez Gene identifiers.")
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Hs.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
(sha256
(base32
"1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
@@ -475,11 +405,7 @@ on mapping using Entrez Gene identifiers.")
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Mm.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
(sha256
(base32
"1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
@@ -501,21 +427,14 @@ annotations for the genome of the model mouse Mus musculus.")
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.UCSC.hg19_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
+ version 'annotation))
(sha256
(base32
"1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
(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
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -555,11 +474,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(source
(origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/experiment/src/contrib"
- "/geneLenDataBase_" version ".tar.gz"))
+ (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
(sha256
(base32
"03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
@@ -582,21 +497,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
(version "3.2.2")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
+ version 'annotation))
(sha256
(base32
"1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
(properties
`((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
(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
`(("r-genomicfeatures" ,r-genomicfeatures)))
(home-page
@@ -614,12 +522,8 @@ track. The database is exposed as a @code{TxDb} object.")
(version "3.4.6")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
+ version 'annotation))
(sha256
(base32
"12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
@@ -643,12 +547,8 @@ track. The database is exposed as a @code{TxDb} object.")
(version "3.2.2")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
+ version 'annotation))
(sha256
(base32
"16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
@@ -673,21 +573,14 @@ database is exposed as a @code{TxDb} object.")
(version "3.4.7")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "TxDb.Mmusculus.UCSC.mm10.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
+ version 'annotation))
(sha256
(base32
"04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(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
`(("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
@@ -733,12 +626,8 @@ by exposing these as TxDb objects.")
(version "2.2.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "FDb.InfiniumMethylation.hg19_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
+ version 'annotation))
(sha256
(base32
"0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
@@ -765,12 +654,8 @@ annotations.")
(version "0.3.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "IlluminaHumanMethylationEPICmanifest_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
+ version 'annotation))
(sha256
(base32
"0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
@@ -791,11 +676,7 @@ annotations.")
(version "2.9")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "DO.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "DO.db" version 'annotation))
(sha256
(base32
"10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
@@ -872,11 +753,7 @@ species.")
(version "1.12.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "ABAData_" version ".tar.gz"))
+ (uri (bioconductor-uri "ABAData" version 'experiment))
(sha256
(base32
"1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
@@ -909,11 +786,7 @@ All datasets are restricted to protein coding genes.")
(version "1.18.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "ARRmData_" version ".tar.gz"))
+ (uri (bioconductor-uri "ARRmData" version 'experiment))
(sha256
(base32
"0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
@@ -933,11 +806,7 @@ from Illumina 450k methylation arrays.")
(version "1.2.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "HSMMSingleCell_" version ".tar.gz"))
+ (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
(sha256
(base32
"1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
@@ -966,11 +835,7 @@ resulting in a complete gene expression profile for each cell.")
(version "1.26.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "ALL_" version ".tar.gz"))
+ (uri (bioconductor-uri "ALL" version 'experiment))
(sha256
(base32
"1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-02 03:46:24 +0000