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authorAndreas Enge <andreas@enge.fr>2023-04-22 09:21:22 +0200
committerAndreas Enge <andreas@enge.fr>2023-04-22 09:21:22 +0200
commitd1252b597d8b6c77746da7b7417d958f00d01dc6 (patch)
treee2cdc9b0938e5ed7ac1b095b83c5760bbedecb87 /gnu/packages/bioinformatics.scm
parent3f7ae420d8a54d4e2ab7f349c40d8930fe9e0771 (diff)
parent040d35f088e0f1c856f3f5a9b6bf889b17bd68b3 (diff)
downloadguix-d1252b597d8b6c77746da7b7417d958f00d01dc6.tar
guix-d1252b597d8b6c77746da7b7417d958f00d01dc6.tar.gz
Merge remote-tracking branch 'origin/master' into core-updates
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm331
1 files changed, 190 insertions, 141 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a986e118f8..68c1406fc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2220,167 +2220,179 @@ easy-to-perform steps.")
(license license:gpl3+)))
(define-public bpp-core
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
- (package
- (name "bpp-core")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-core")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "C++ libraries for Bioinformatics")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-core")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-core")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"))))
+ (build-system cmake-build-system)
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-core/html/index.html")
+ (synopsis "C++ libraries for Bioinformatics")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. It is
Object Oriented and is designed to be both easy to use and computer efficient.
Bio++ intends to help programmers to write computer expensive programs, by
providing them a set of re-usable tools.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-phyl
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
- (package
- (name "bpp-phyl")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ phylogenetic Library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-phyl")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/")
+ (synopsis "Bio++ phylogenetic library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides phylogenetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
+
+(define-public bpp-phyl-omics
+ (package
+ (name "bpp-phyl-omics")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-phyl-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "172psb8njkjwg3cd6gdy5w0mq8f0817v635yw4bk7146aggjzl1h"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; No test provided.
+ (inputs
+ (list bpp-core
+ bpp-phyl
+ bpp-seq
+ bpp-seq-omics))
+ (home-page "https://github.com/BioPP/bpp-phyl-omics")
+ (synopsis "Bio++ phylogenetic library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ phylogenetics
+library. It is part of the Bio++ project.")
+ (license license:cecill)))
(define-public bpp-popgen
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
- (package
- (name "bpp-popgen")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- #:tests? #f)) ; There are no tests.
- (inputs
- (list bpp-core bpp-seq))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ population genetics library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-popgen")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-popgen")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests.
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/")
+ (synopsis "Bio++ population genetics library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides population genetics-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public bpp-seq
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
- (package
- (name "bpp-seq")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bpp-seq")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- ;; If out-of-source, test data is not copied into the build directory
- ;; so the tests fail.
- #:out-of-source? #f))
- (inputs
- (list bpp-core))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bio++ sequence library")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bpp-seq")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core))
+ (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/")
+ (synopsis "Bio++ sequence library")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides sequence-related modules.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
+
+(define-public bpp-seq-omics
+ (package
+ (name "bpp-seq-omics")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bpp-seq-omics")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sc2xdfnfp5a6qihplp49rgrqmj89898avfy9bqaq1g2fajppgjj"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list bpp-core bpp-seq))
+ (home-page "https://github.com/BioPP/bpp-seq-omics")
+ (synopsis "Bio++ sequence library genomics components")
+ (description
+ "This library contains the genomics components of the Bio++ sequence library.
+It is part of the Bio++ project.")
+ (license license:cecill)))
(define-public bppsuite
- ;; The last release was in 2014 and the recommended way to install from source
- ;; is to clone the git repository, so we do this.
- ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
- (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
- (package
- (name "bppsuite")
- (version (string-append "2.2.0-1." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "http://biopp.univ-montp2.fr/git/bppsuite")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
- (build-system cmake-build-system)
- (arguments
- `(#:parallel-build? #f
- #:tests? #f)) ; There are no tests.
- (native-inputs
- (list groff man-db texinfo))
- (inputs
- `(("bpp-core" ,bpp-core)
- ("bpp-seq" ,bpp-seq)
- ("bpp-phyl" ,bpp-phyl)
- ("bpp-phyl" ,bpp-popgen)))
- (home-page "http://biopp.univ-montp2.fr")
- (synopsis "Bioinformatics tools written with the Bio++ libraries")
- (description
- "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ (package
+ (name "bppsuite")
+ (version "2.4.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BioPP/bppsuite")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests.
+ (native-inputs
+ (list groff man-db texinfo))
+ (inputs
+ (list bpp-core bpp-seq bpp-phyl bpp-popgen))
+ (home-page "https://github.com/BioPP")
+ (synopsis "Bioinformatics tools written with the Bio++ libraries")
+ (description
+ "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
package provides command line tools using the Bio++ library.")
- (license license:cecill-c))))
+ (license license:cecill-c)))
(define-public blast+
(package
@@ -6021,6 +6033,43 @@ resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public maffilter
+ (package
+ (name "maffilter")
+ (version "1.3.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jydu/maffilter")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "196c16qw82niqqyzi7j1ga1n0zmir73bm26kg04m0i5aq2cpa0ml"))))
+ (build-system cmake-build-system)
+ (arguments (list #:tests? #false)) ;there are none
+ (inputs
+ (list boost
+ bpp-core
+ bpp-phyl
+ bpp-phyl-omics
+ bpp-seq
+ bpp-seq-omics
+ zlib))
+ (home-page "https://jydu.github.io/maffilter/")
+ (synopsis "Multiple alignment format file processor")
+ (description
+ "MafFilter is a program dedicated to the analysis of genome alignments.
+It parses and manipulates @acronym{MAF, multiple alignment format} files as
+well as more simple fasta files. This package can be used to design a
+pipeline as a series of consecutive filters, each performing a dedicated
+analysis. Many of the filters are available, from alignment cleaning to
+phylogeny reconstruction and population genetics analysis. Despite various
+filtering options and format conversion tools, MafFilter can compute a wide
+range of statistics (phylogenetic trees, nucleotide diversity, inferrence of
+selection, etc.).")
+ (license license:gpl3+)))
+
(define-public mafft
(package
(name "mafft")