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:
Marius Bakke
commit
462ad9f56b
108 changed files with 7403 additions and 3423 deletions
|
|
@ -13,6 +13,7 @@
|
|||
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
|
||||
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
|
||||
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
|
||||
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
|
|
@ -4195,8 +4196,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
|
|||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'set-cc
|
||||
(lambda _ (setenv "CC" "gcc") #t))
|
||||
;; FIXME: This fails with "permission denied".
|
||||
(delete 'reset-gzip-timestamps))))
|
||||
|
||||
(add-before 'reset-gzip-timestamps 'make-files-writable
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
;; Make sure .gz files are writable so that the
|
||||
;; 'reset-gzip-timestamps' phase can do its work.
|
||||
(let ((out (assoc-ref outputs "out")))
|
||||
(for-each make-file-writable
|
||||
(find-files out "\\.gz$"))
|
||||
#t))))))
|
||||
(native-inputs
|
||||
`(("python-cython" ,python-cython)
|
||||
("python-pytest" ,python-pytest)
|
||||
|
|
@ -7439,13 +7447,13 @@ names in their natural, rather than lexicographic, order.")
|
|||
(define-public r-edger
|
||||
(package
|
||||
(name "r-edger")
|
||||
(version "3.26.5")
|
||||
(version "3.26.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "edgeR" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
|
||||
"17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
|
||||
(properties `((upstream-name . "edgeR")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -7506,13 +7514,13 @@ coding changes and predict coding outcomes.")
|
|||
(define-public r-limma
|
||||
(package
|
||||
(name "r-limma")
|
||||
(version "3.40.2")
|
||||
(version "3.40.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "limma" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
|
||||
"166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://bioinf.wehi.edu.au/limma")
|
||||
(synopsis "Package for linear models for microarray and RNA-seq data")
|
||||
|
|
@ -7639,13 +7647,13 @@ annotation data packages using SQLite data storage.")
|
|||
(define-public r-biomart
|
||||
(package
|
||||
(name "r-biomart")
|
||||
(version "2.40.1")
|
||||
(version "2.40.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "biomaRt" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
|
||||
"022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
|
||||
(properties
|
||||
`((upstream-name . "biomaRt")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -7672,13 +7680,13 @@ powerful online queries from gene annotation to database mining.")
|
|||
(define-public r-biocparallel
|
||||
(package
|
||||
(name "r-biocparallel")
|
||||
(version "1.18.0")
|
||||
(version "1.18.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "BiocParallel" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
|
||||
"1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3"))))
|
||||
(properties
|
||||
`((upstream-name . "BiocParallel")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -7800,13 +7808,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
|
|||
(define-public r-summarizedexperiment
|
||||
(package
|
||||
(name "r-summarizedexperiment")
|
||||
(version "1.14.0")
|
||||
(version "1.14.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "SummarizedExperiment" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
|
||||
"0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
|
||||
(properties
|
||||
`((upstream-name . "SummarizedExperiment")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -7864,13 +7872,13 @@ alignments.")
|
|||
(define-public r-rtracklayer
|
||||
(package
|
||||
(name "r-rtracklayer")
|
||||
(version "1.44.0")
|
||||
(version "1.44.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "rtracklayer" version))
|
||||
(sha256
|
||||
(base32
|
||||
"161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
|
||||
"03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
|
|
@ -7911,13 +7919,13 @@ as well as query and modify the browser state, such as the current viewport.")
|
|||
(define-public r-genomicfeatures
|
||||
(package
|
||||
(name "r-genomicfeatures")
|
||||
(version "1.36.3")
|
||||
(version "1.36.4")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "GenomicFeatures" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
|
||||
"0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
|
||||
(properties
|
||||
`((upstream-name . "GenomicFeatures")))
|
||||
(build-system r-build-system)
|
||||
|
|
@ -8335,13 +8343,13 @@ paired-end data.")
|
|||
(define-public r-rcas
|
||||
(package
|
||||
(name "r-rcas")
|
||||
(version "1.10.0")
|
||||
(version "1.10.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "RCAS" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
|
||||
"06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
|
||||
(properties `((upstream-name . "RCAS")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -9399,14 +9407,14 @@ of mass spectrometry based proteomics data.")
|
|||
(define-public r-msnid
|
||||
(package
|
||||
(name "r-msnid")
|
||||
(version "1.18.0")
|
||||
(version "1.18.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "MSnID" version))
|
||||
(sha256
|
||||
(base32
|
||||
"18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
|
||||
"1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
|
||||
(properties `((upstream-name . "MSnID")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
|
|
@ -10406,14 +10414,14 @@ provided.")
|
|||
(define-public r-hdf5array
|
||||
(package
|
||||
(name "r-hdf5array")
|
||||
(version "1.12.1")
|
||||
(version "1.12.2")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "HDF5Array" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp"))))
|
||||
"0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5"))))
|
||||
(properties `((upstream-name . "HDF5Array")))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
|
|
@ -14804,3 +14812,406 @@ trees by inserting random mutations. The tbsp package implements an
|
|||
alternative method to detect significant, cell type specific sequence
|
||||
mutations from scRNA-Seq data.")
|
||||
(license license:expat))))
|
||||
|
||||
(define-public tabixpp
|
||||
(package
|
||||
(name "tabixpp")
|
||||
(version "1.0.0")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/tabixpp")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("htslib" ,htslib)
|
||||
("zlib" ,zlib)))
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests to run.
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; There is no configure phase.
|
||||
;; The build phase needs overriding the location of htslib.
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((htslib-ref (assoc-ref inputs "htslib")))
|
||||
(invoke "make"
|
||||
(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
|
||||
"HTS_HEADERS=" ; No need to check for headers here.
|
||||
(string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "tabix++" bin))
|
||||
#t)))))
|
||||
(home-page "https://github.com/ekg/tabixpp")
|
||||
(synopsis "C++ wrapper around tabix project")
|
||||
(description "This is a C++ wrapper around the Tabix project which abstracts
|
||||
some of the details of opening and jumping in tabix-indexed files.")
|
||||
(license license:expat)))
|
||||
|
||||
(define tabixpp-freebayes
|
||||
;; This version works with FreeBayes while the released
|
||||
;; version doesn't. The released creates a variable with the name \"vcf\"
|
||||
;; somewhere, which is also the name of a namespace in vcflib.
|
||||
(let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
|
||||
(package
|
||||
(inherit tabixpp)
|
||||
(name "tabixpp-freebayes")
|
||||
(version (git-version "0.0.0" "1" commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/tabixpp/")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
|
||||
|
||||
(define-public smithwaterman
|
||||
;; TODO: Upgrading smithwaterman breaks FreeBayes.
|
||||
(let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
|
||||
(package
|
||||
(name "smithwaterman")
|
||||
(version (string-append "0-1." (string-take commit 7)))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/smithwaterman/")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests to run.
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; There is no configure phase.
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "smithwaterman" bin))
|
||||
#t)))))
|
||||
(home-page "https://github.com/ekg/smithwaterman")
|
||||
(synopsis "Implementation of the Smith-Waterman algorithm")
|
||||
(description "Implementation of the Smith-Waterman algorithm.")
|
||||
;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
|
||||
(license (list license:gpl2 license:expat)))))
|
||||
|
||||
(define-public multichoose
|
||||
(package
|
||||
(name "multichoose")
|
||||
(version "1.0.3")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/multichoose/")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; Tests require node.
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; There is no configure phase.
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
;; TODO: There are Python modules for these programs too.
|
||||
(install-file "multichoose" bin)
|
||||
(install-file "multipermute" bin))
|
||||
#t)))))
|
||||
(home-page "https://github.com/ekg/multichoose")
|
||||
(synopsis "Efficient loopless multiset combination generation algorithm")
|
||||
(description "This library implements an efficient loopless multiset
|
||||
combination generation algorithm which is (approximately) described in
|
||||
\"Loopless algorithms for generating permutations, combinations, and other
|
||||
combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
|
||||
1973. (Algorithm 7.)")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public fsom
|
||||
(let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
|
||||
(package
|
||||
(name "fsom")
|
||||
(version (git-version "0.0.0" "1" commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/fsom/")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests to run.
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; There is no configure phase.
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "fsom" bin))
|
||||
#t)))))
|
||||
(home-page "https://github.com/ekg/fsom")
|
||||
(synopsis "Manage SOM (Self-Organizing Maps) neural networks")
|
||||
(description "A tiny C library for managing SOM (Self-Organizing Maps)
|
||||
neural networks.")
|
||||
(license license:gpl3))))
|
||||
|
||||
(define-public fastahack
|
||||
(let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
|
||||
(package
|
||||
(name "fastahack")
|
||||
(version (git-version "0.0.0" "1" commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/fastahack/")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; There is no configure phase.
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "fastahack" bin))
|
||||
#t)))))
|
||||
(home-page "https://github.com/ekg/fastahack")
|
||||
(synopsis "Indexing and sequence extraction from FASTA files")
|
||||
(description "Fastahack is a small application for indexing and
|
||||
extracting sequences and subsequences from FASTA files. The included library
|
||||
provides a FASTA reader and indexer that can be embedded into applications
|
||||
which would benefit from directly reading subsequences from FASTA files. The
|
||||
library automatically handles index file generation and use.")
|
||||
(license (list license:expat license:gpl2)))))
|
||||
|
||||
(define-public vcflib
|
||||
(let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
|
||||
(revision "1"))
|
||||
(package
|
||||
(name "vcflib")
|
||||
(version (git-version "0.0.0" revision commit))
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/vcflib/vcflib/")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("perl" ,perl)
|
||||
("python" ,python-2)
|
||||
;; Submodules.
|
||||
;; This package builds against the .o files so we need to extract the source.
|
||||
("tabixpp-src" ,(package-source tabixpp-freebayes))
|
||||
("smithwaterman-src" ,(package-source smithwaterman))
|
||||
("multichoose-src" ,(package-source multichoose))
|
||||
("fsom-src" ,(package-source fsom))
|
||||
("filevercmp-src" ,(package-source filevercmp))
|
||||
("fastahack-src" ,(package-source fastahack))
|
||||
("intervaltree-src"
|
||||
,(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/intervaltree/")
|
||||
(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
|
||||
(file-name "intervaltree-src-checkout")
|
||||
(sha256
|
||||
(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
|
||||
(arguments
|
||||
`(#:tests? #f ; no tests
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(delete 'check)
|
||||
(add-after 'unpack 'unpack-submodule-sources
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((unpack (lambda (source target)
|
||||
(with-directory-excursion target
|
||||
(if (file-is-directory? (assoc-ref inputs source))
|
||||
(copy-recursively (assoc-ref inputs source) ".")
|
||||
(invoke "tar" "xvf"
|
||||
(assoc-ref inputs source)
|
||||
"--strip-components=1"))))))
|
||||
(and
|
||||
(unpack "intervaltree-src" "intervaltree")
|
||||
(unpack "fastahack-src" "fastahack")
|
||||
(unpack "filevercmp-src" "filevercmp")
|
||||
(unpack "fsom-src" "fsom")
|
||||
(unpack "multichoose-src" "multichoose")
|
||||
(unpack "smithwaterman-src" "smithwaterman")
|
||||
(unpack "tabixpp-src" "tabixpp")))))
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs make-flags #:allow-other-keys)
|
||||
(with-directory-excursion "tabixpp"
|
||||
(invoke "make"))
|
||||
(invoke "make" "CC=gcc"
|
||||
(string-append "CFLAGS=\"" "-Itabixpp " "\"")
|
||||
"all")))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
|
||||
(lib (string-append (assoc-ref outputs "out") "/lib")))
|
||||
(for-each (lambda (file)
|
||||
(install-file file bin))
|
||||
(find-files "bin" ".*"))
|
||||
;; The header files in src/ do not interface libvcflib,
|
||||
;; therefore they are left out.
|
||||
(install-file "libvcflib.a" lib))
|
||||
#t)))))
|
||||
(home-page "https://github.com/vcflib/vcflib/")
|
||||
(synopsis "Library for parsing and manipulating VCF files")
|
||||
(description "Vcflib provides methods to manipulate and interpret
|
||||
sequence variation as it can be described by VCF. It is both an API for parsing
|
||||
and operating on records of genomic variation as it can be described by the VCF
|
||||
format, and a collection of command-line utilities for executing complex
|
||||
manipulations on VCF files.")
|
||||
(license license:expat))))
|
||||
|
||||
(define-public freebayes
|
||||
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
|
||||
(revision "1")
|
||||
(version "1.0.2"))
|
||||
(package
|
||||
(name "freebayes")
|
||||
(version (git-version version revision commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/freebayes.git")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("bamtools" ,bamtools)
|
||||
("htslib" ,htslib)
|
||||
("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("bc" ,bc) ; Needed for running tests.
|
||||
("samtools" ,samtools) ; Needed for running tests.
|
||||
("parallel" ,parallel) ; Needed for running tests.
|
||||
("perl" ,perl) ; Needed for running tests.
|
||||
("procps" ,procps) ; Needed for running tests.
|
||||
("python" ,python-2) ; Needed for running tests.
|
||||
("vcflib-src" ,(package-source vcflib))
|
||||
;; These are submodules for the vcflib version used in freebayes.
|
||||
;; This package builds against the .o files so we need to extract the source.
|
||||
("tabixpp-src" ,(package-source tabixpp-freebayes))
|
||||
("smithwaterman-src" ,(package-source smithwaterman))
|
||||
("multichoose-src" ,(package-source multichoose))
|
||||
("fsom-src" ,(package-source fsom))
|
||||
("filevercmp-src" ,(package-source filevercmp))
|
||||
("fastahack-src" ,(package-source fastahack))
|
||||
("intervaltree-src"
|
||||
,(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/intervaltree/")
|
||||
(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
|
||||
(file-name "intervaltree-src-checkout")
|
||||
(sha256
|
||||
(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
|
||||
;; These submodules are needed to run the tests.
|
||||
("bash-tap-src" ,(package-source bash-tap))
|
||||
("test-simple-bash-src"
|
||||
,(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ingydotnet/test-simple-bash/")
|
||||
(commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
|
||||
(file-name "test-simple-bash-src-checkout")
|
||||
(sha256
|
||||
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
|
||||
(arguments
|
||||
`(#:make-flags
|
||||
(list "CC=gcc"
|
||||
(string-append "BAMTOOLS_ROOT="
|
||||
(assoc-ref %build-inputs "bamtools")))
|
||||
#:test-target "test"
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(add-after 'unpack 'fix-tests
|
||||
(lambda _
|
||||
(substitute* "test/t/01_call_variants.t"
|
||||
(("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
|
||||
"grep -E ' (500|11000|1000)$'"))
|
||||
#t))
|
||||
(add-after 'unpack 'unpack-submodule-sources
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((unpack (lambda (source target)
|
||||
(with-directory-excursion target
|
||||
(if (file-is-directory? (assoc-ref inputs source))
|
||||
(copy-recursively (assoc-ref inputs source) ".")
|
||||
(invoke "tar" "xvf"
|
||||
(assoc-ref inputs source)
|
||||
"--strip-components=1"))))))
|
||||
(and
|
||||
(unpack "vcflib-src" "vcflib")
|
||||
(unpack "fastahack-src" "vcflib/fastahack")
|
||||
(unpack "filevercmp-src" "vcflib/filevercmp")
|
||||
(unpack "fsom-src" "vcflib/fsom")
|
||||
(unpack "intervaltree-src" "vcflib/intervaltree")
|
||||
(unpack "multichoose-src" "vcflib/multichoose")
|
||||
(unpack "smithwaterman-src" "vcflib/smithwaterman")
|
||||
(unpack "tabixpp-src" "vcflib/tabixpp")
|
||||
(unpack "test-simple-bash-src" "test/test-simple-bash")
|
||||
(unpack "bash-tap-src" "test/bash-tap")))))
|
||||
(add-after 'unpack-submodule-sources 'fix-makefiles
|
||||
(lambda _
|
||||
;; We don't have the .git folder to get the version tag from.
|
||||
(substitute* "vcflib/Makefile"
|
||||
(("^GIT_VERSION.*")
|
||||
(string-append "GIT_VERSION = v" ,version)))
|
||||
(substitute* "src/Makefile"
|
||||
(("-I\\$\\(BAMTOOLS_ROOT\\)/src")
|
||||
"-I$(BAMTOOLS_ROOT)/include/bamtools"))
|
||||
#t))
|
||||
(add-before 'build 'build-tabixpp-and-vcflib
|
||||
(lambda* (#:key inputs make-flags #:allow-other-keys)
|
||||
(with-directory-excursion "vcflib"
|
||||
(with-directory-excursion "tabixpp"
|
||||
(apply invoke "make"
|
||||
(string-append "HTS_LIB="
|
||||
(assoc-ref inputs "htslib")
|
||||
"/lib/libhts.a")
|
||||
make-flags))
|
||||
(apply invoke "make"
|
||||
(string-append "CFLAGS=-Itabixpp")
|
||||
"all"
|
||||
make-flags))))
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "bin/freebayes" bin)
|
||||
(install-file "bin/bamleftalign" bin))
|
||||
#t)))))
|
||||
(home-page "https://github.com/ekg/freebayes")
|
||||
(synopsis "Haplotype-based variant detector")
|
||||
(description "FreeBayes is a Bayesian genetic variant detector designed to
|
||||
find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
|
||||
indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
|
||||
complex events (composite insertion and substitution events) smaller than the
|
||||
length of a short-read sequencing alignment.")
|
||||
(license license:expat))))
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue