mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
Merge branch 'master' into core-updates
This commit is contained in:
Mark H Weaver
commit
3d5ad159b3
105 changed files with 29149 additions and 23582 deletions
|
|
@ -252,7 +252,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
|
|||
(define-public bamtools
|
||||
(package
|
||||
(name "bamtools")
|
||||
(version "2.4.1")
|
||||
(version "2.5.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -261,7 +261,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk"))))
|
||||
"1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ;no "check" target
|
||||
|
|
@ -285,7 +285,7 @@ BAM files.")
|
|||
(define-public bcftools
|
||||
(package
|
||||
(name "bcftools")
|
||||
(version "1.5")
|
||||
(version "1.8")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -293,12 +293,11 @@ BAM files.")
|
|||
version "/bcftools-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
|
||||
(patches (search-patches "bcftools-regidx-unsigned-char.patch"))
|
||||
"1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet '(begin
|
||||
;; Delete bundled htslib.
|
||||
(delete-file-recursively "htslib-1.5")
|
||||
(delete-file-recursively "htslib-1.8")
|
||||
#t))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
|
|
@ -339,7 +338,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
|
|||
(define-public bedops
|
||||
(package
|
||||
(name "bedops")
|
||||
(version "2.4.14")
|
||||
(version "2.4.33")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/bedops/bedops/archive/v"
|
||||
|
|
@ -347,7 +346,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
|
||||
"0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f
|
||||
|
|
@ -2089,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.")
|
|||
(define-public diamond
|
||||
(package
|
||||
(name "diamond")
|
||||
(version "0.9.19")
|
||||
(version "0.9.21")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -2098,7 +2097,7 @@ accurately delineate genomic rearrangements throughout the genome.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0c4y8l90vdxmglb0w37y0413v11qzcwg8sdmy9k0c0gr3bsq7dzs"))))
|
||||
"1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f ; no "check" target
|
||||
|
|
@ -2349,7 +2348,8 @@ dynamic programming or a variety of heuristics.")
|
|||
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
|
||||
(substitute* "src/CMakeLists.txt"
|
||||
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
|
||||
(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
|
||||
(string-append (assoc-ref inputs "bamtools") "/lib"))
|
||||
(("libprotobuf.a") "libprotobuf.so"))
|
||||
#t)))))
|
||||
(inputs
|
||||
`(("boost" ,boost)
|
||||
|
|
@ -3462,7 +3462,7 @@ The main functions of FastQC are:
|
|||
(define-public htslib
|
||||
(package
|
||||
(name "htslib")
|
||||
(version "1.7")
|
||||
(version "1.8")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
|
|
@ -3470,7 +3470,7 @@ The main functions of FastQC are:
|
|||
version "/htslib-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy"))))
|
||||
"18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("openssl" ,openssl)
|
||||
|
|
@ -4587,7 +4587,7 @@ partial genes, and identifies translation initiation sites.")
|
|||
(define-public roary
|
||||
(package
|
||||
(name "roary")
|
||||
(version "3.11.0")
|
||||
(version "3.12.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -4596,7 +4596,7 @@ partial genes, and identifies translation initiation sites.")
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
|
||||
"0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
|
||||
(build-system perl-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
|
|
@ -4934,7 +4934,7 @@ to the user's query of interest.")
|
|||
(define-public samtools
|
||||
(package
|
||||
(name "samtools")
|
||||
(version "1.7")
|
||||
(version "1.8")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -4943,7 +4943,7 @@ to the user's query of interest.")
|
|||
version "/samtools-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77"))))
|
||||
"05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:modules ((ice-9 ftw)
|
||||
|
|
@ -5784,7 +5784,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
|
|||
(define-public star
|
||||
(package
|
||||
(name "star")
|
||||
(version "2.5.3a")
|
||||
(version "2.6.0a")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
|
||||
|
|
@ -5792,7 +5792,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
|
||||
"0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
|
|
@ -5979,13 +5979,13 @@ Cuffdiff or Ballgown programs.")
|
|||
(define-public taxtastic
|
||||
(package
|
||||
(name "taxtastic")
|
||||
(version "0.6.4")
|
||||
(version "0.8.5")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "taxtastic" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929"))))
|
||||
"03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:python ,python-2
|
||||
|
|
@ -6098,19 +6098,20 @@ information as possible.")
|
|||
(define-public r-vegan
|
||||
(package
|
||||
(name "r-vegan")
|
||||
(version "2.4-6")
|
||||
(version "2.5-1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "vegan" version))
|
||||
(sha256
|
||||
(base32
|
||||
"175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
|
||||
"0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r"))))
|
||||
(build-system r-build-system)
|
||||
(native-inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(propagated-inputs
|
||||
`(("r-cluster" ,r-cluster)
|
||||
("r-knitr" ,r-knitr)
|
||||
("r-lattice" ,r-lattice)
|
||||
("r-mass" ,r-mass)
|
||||
("r-mgcv" ,r-mgcv)
|
||||
|
|
@ -6266,14 +6267,14 @@ distribution.")
|
|||
(define-public r-dexseq
|
||||
(package
|
||||
(name "r-dexseq")
|
||||
(version "1.24.3")
|
||||
(version "1.24.4")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "DEXSeq" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"))))
|
||||
"1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"))))
|
||||
(properties `((upstream-name . "DEXSeq")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -6619,7 +6620,7 @@ SELECT or UPDATE queries to an end-point.")
|
|||
(define-public vsearch
|
||||
(package
|
||||
(name "vsearch")
|
||||
(version "2.7.1")
|
||||
(version "2.8.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -6629,7 +6630,7 @@ SELECT or UPDATE queries to an end-point.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f"))
|
||||
"15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
|
||||
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
|
||||
(snippet
|
||||
'(begin
|
||||
|
|
@ -7604,13 +7605,13 @@ samples.")
|
|||
(define-public r-genomicalignments
|
||||
(package
|
||||
(name "r-genomicalignments")
|
||||
(version "1.14.1")
|
||||
(version "1.14.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GenomicAlignments" version))
|
||||
(sha256
|
||||
(base32
|
||||
"033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39"))))
|
||||
"1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
|
||||
(properties
|
||||
`((upstream-name . "GenomicAlignments")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -9077,14 +9078,14 @@ replacement for strverscmp.")
|
|||
(define-public multiqc
|
||||
(package
|
||||
(name "multiqc")
|
||||
(version "1.4")
|
||||
(version "1.5")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "multiqc" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8"))))
|
||||
"02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
|
||||
(build-system python-build-system)
|
||||
(propagated-inputs
|
||||
`(("python-jinja2" ,python-jinja2)
|
||||
|
|
@ -9652,13 +9653,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
|
|||
(define-public r-seurat
|
||||
(package
|
||||
(name "r-seurat")
|
||||
(version "2.2.1")
|
||||
(version "2.3.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "Seurat" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2"))
|
||||
"0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0"))
|
||||
;; Delete pre-built jar.
|
||||
(snippet
|
||||
'(begin (delete-file "inst/java/ModularityOptimizer.jar")
|
||||
|
|
@ -9688,11 +9689,15 @@ Main-Class: ModularityOptimizer\n")))
|
|||
(propagated-inputs
|
||||
`(("r-ape" ,r-ape)
|
||||
("r-caret" ,r-caret)
|
||||
("r-cluster" ,r-cluster)
|
||||
("r-cowplot" ,r-cowplot)
|
||||
("r-diffusionmap" ,r-diffusionmap)
|
||||
("r-dosnow" ,r-dosnow)
|
||||
("r-dplyr" ,r-dplyr)
|
||||
("r-dtw" ,r-dtw)
|
||||
("r-fitdistrplus" ,r-fitdistrplus)
|
||||
("r-fnn" ,r-fnn)
|
||||
("r-foreach" ,r-foreach)
|
||||
("r-fpc" ,r-fpc)
|
||||
("r-gdata" ,r-gdata)
|
||||
("r-ggplot2" ,r-ggplot2)
|
||||
|
|
@ -9704,13 +9709,16 @@ Main-Class: ModularityOptimizer\n")))
|
|||
("r-igraph" ,r-igraph)
|
||||
("r-irlba" ,r-irlba)
|
||||
("r-lars" ,r-lars)
|
||||
("r-lmtest" ,r-lmtest)
|
||||
("r-mass" ,r-mass)
|
||||
("r-matrix" ,r-matrix)
|
||||
("r-metap" ,r-metap)
|
||||
("r-mixtools" ,r-mixtools)
|
||||
("r-pbapply" ,r-pbapply)
|
||||
("r-plotly" ,r-plotly)
|
||||
("r-png" ,r-png)
|
||||
("r-ranger" ,r-ranger)
|
||||
("r-rann" ,r-rann)
|
||||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||||
("r-rcpp" ,r-rcpp)
|
||||
("r-rcppeigen" ,r-rcppeigen)
|
||||
|
|
@ -10185,14 +10193,14 @@ effort and encourages consistency.")
|
|||
(define-public r-ggbio
|
||||
(package
|
||||
(name "r-ggbio")
|
||||
(version "1.26.0")
|
||||
(version "1.26.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "ggbio" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9"))))
|
||||
"1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-annotationdbi" ,r-annotationdbi)
|
||||
|
|
@ -10237,14 +10245,14 @@ interval to data view, mismatch pileup, and several splicing summaries.")
|
|||
(define-public r-gprofiler
|
||||
(package
|
||||
(name "r-gprofiler")
|
||||
(version "0.6.4")
|
||||
(version "0.6.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "gProfileR" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b"))))
|
||||
"1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi"))))
|
||||
(properties `((upstream-name . "gProfileR")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -10355,14 +10363,14 @@ several related annotation packages.")
|
|||
(define-public r-erma
|
||||
(package
|
||||
(name "r-erma")
|
||||
(version "0.10.0")
|
||||
(version "0.10.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "erma" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"))))
|
||||
"1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-annotationdbi" ,r-annotationdbi)
|
||||
|
|
@ -10391,14 +10399,14 @@ by Ernst and Kellis.")
|
|||
(define-public r-ldblock
|
||||
(package
|
||||
(name "r-ldblock")
|
||||
(version "1.8.0")
|
||||
(version "1.8.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "ldblock" version))
|
||||
(sha256
|
||||
(base32
|
||||
"18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"))))
|
||||
"1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-erma" ,r-erma)
|
||||
|
|
@ -10608,13 +10616,13 @@ assays such as Hi-C.")
|
|||
(define-public r-hitc
|
||||
(package
|
||||
(name "r-hitc")
|
||||
(version "1.22.0")
|
||||
(version "1.22.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "HiTC" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp"))))
|
||||
"0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"))))
|
||||
(properties `((upstream-name . "HiTC")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -10856,14 +10864,14 @@ quality control.")
|
|||
(define-public r-scran
|
||||
(package
|
||||
(name "r-scran")
|
||||
(version "1.6.8")
|
||||
(version "1.6.9")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "scran" version))
|
||||
(sha256
|
||||
(base32
|
||||
"07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x"))))
|
||||
"0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-beachmat" ,r-beachmat)
|
||||
|
|
@ -12826,7 +12834,7 @@ expression report comparing samples in an easily configurable manner.")
|
|||
(define-public pigx-chipseq
|
||||
(package
|
||||
(name "pigx-chipseq")
|
||||
(version "0.0.10")
|
||||
(version "0.0.15")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
|
||||
|
|
@ -12834,7 +12842,7 @@ expression report comparing samples in an easily configurable manner.")
|
|||
"/pigx_chipseq-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"13w99bkr0w4j28ms0yzpl1x6fkpdqay0vh495q3x20bcilsjwnf1"))))
|
||||
"11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; parts of the tests rely on access to the network
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue