diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 331 |
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") |