diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 178 |
1 files changed, 172 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 956257d7bb..e860b5b881 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,13 +7691,13 @@ 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) @@ -10425,14 +10425,14 @@ 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 @@ -13964,13 +13964,11 @@ datasets.") ("ghc-intervalmap" ,ghc-intervalmap) ("ghc-missingh" ,ghc-missingh) ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-parsec" ,ghc-parsec) ("ghc-regex" ,ghc-regex) ("ghc-safe" ,ghc-safe) ("ghc-safeio" ,ghc-safeio) ("ghc-strict" ,ghc-strict) ("ghc-tar" ,ghc-tar) - ("ghc-text" ,ghc-text) ("ghc-unliftio" ,ghc-unliftio) ("ghc-unliftio-core" ,ghc-unliftio-core) ("ghc-vector" ,ghc-vector) @@ -14829,3 +14827,171 @@ 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-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))))) |