mirror of
git://git.savannah.gnu.org/guix.git
synced 2023-12-14 03:33:07 +01:00
gnu: vcflib: Update to 1.0.1.
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.1. [source]: Download using url-fetch. [native-inputs]: Sort alphabetically. Move perl, python ... [inputs]: ... to here. [arguments]: Add make-flags. Update custom 'build phase. (tabixpp-freebayes): Remove variable. (freebayes)[native-inputs]: Use tabixpp-source over tabixpp-freebayes.
This commit is contained in:
parent
2e3efa6e55
commit
0ab7f6c5f4
GPG key ID:
41AAE7DCCA3D8351
1 changed files with 93 additions and 92 deletions
|
|
@ -14941,24 +14941,6 @@ mutations from scRNA-Seq data.")
|
|||
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"))
|
||||
|
|
@ -15087,84 +15069,103 @@ 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" ,(package-source intervaltree))))
|
||||
(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)
|
||||
(package
|
||||
(name "vcflib")
|
||||
(version "1.0.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/vcflib/vcflib/releases/"
|
||||
"download/v" version
|
||||
"/vcflib-" version "-src.tar.gz"))
|
||||
(sha256
|
||||
(base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
`(begin
|
||||
(for-each delete-file-recursively
|
||||
'("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
|
||||
"libVCFH" "multichoose" "smithwaterman" "tabixpp"))
|
||||
#t))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(("htslib" ,htslib)
|
||||
("perl" ,perl)
|
||||
("python" ,python)
|
||||
("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(;; Submodules.
|
||||
;; This package builds against the .o files so we need to extract the source.
|
||||
("fastahack-src" ,(package-source fastahack))
|
||||
("filevercmp-src" ,(package-source filevercmp))
|
||||
("fsom-src" ,(package-source fsom))
|
||||
("intervaltree-src" ,(package-source intervaltree))
|
||||
("multichoose-src" ,(package-source multichoose))
|
||||
("smithwaterman-src" ,(package-source smithwaterman))
|
||||
("tabixpp-src" ,(package-source tabixpp))))
|
||||
(arguments
|
||||
`(#:tests? #f ; no tests
|
||||
#:make-flags (list (string-append "HTS_LIB="
|
||||
(assoc-ref %build-inputs "htslib")
|
||||
"/lib/libhts.a")
|
||||
(string-append "HTS_INCLUDES= -I"
|
||||
(assoc-ref %build-inputs "htslib")
|
||||
"/include/htslib")
|
||||
(string-append "HTS_LDFLAGS= -L"
|
||||
(assoc-ref %build-inputs "htslib")
|
||||
"/include/htslib" " -lhts"))
|
||||
#: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)
|
||||
(mkdir 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 "fastahack-src" "fastahack")
|
||||
(unpack "filevercmp-src" "filevercmp")
|
||||
(unpack "fsom-src" "fsom")
|
||||
(unpack "intervaltree-src" "intervaltree")
|
||||
(unpack "multichoose-src" "multichoose")
|
||||
(unpack "smithwaterman-src" "smithwaterman")
|
||||
(unpack "tabixpp-src" "tabixpp")))))
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs make-flags #:allow-other-keys)
|
||||
(let ((htslib (assoc-ref inputs "htslib")))
|
||||
(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
|
||||
(substitute* "Makefile"
|
||||
(("-Ihtslib") (string-append "-I" htslib "/include/htslib"))
|
||||
(("-Lhtslib") (string-append "-L" htslib "/lib/htslib"))
|
||||
(("htslib/htslib") (string-append htslib "/include/htslib")))
|
||||
(invoke "make"
|
||||
(string-append "HTS_LIB=" htslib "/lib/libhts.a")))
|
||||
(apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags))))
|
||||
(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))))
|
||||
(license license:expat)))
|
||||
|
||||
(define-public freebayes
|
||||
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
|
||||
|
|
@ -15196,7 +15197,7 @@ manipulations on VCF files.")
|
|||
("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))
|
||||
("tabixpp-src" ,(package-source tabixpp))
|
||||
("smithwaterman-src" ,(package-source smithwaterman))
|
||||
("multichoose-src" ,(package-source multichoose))
|
||||
("fsom-src" ,(package-source fsom))
|
||||
|
|
|
|||
Loading…
Reference in a new issue