diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 104 |
1 files changed, 94 insertions, 10 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2f3b807c3..32603ae57e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -730,14 +730,14 @@ provide a coordinated and extensible framework to do computational biology.") (define-public python-biopython (package (name "python-biopython") - (version "1.68") + (version "1.70") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "07qc7nz0k77y8hf8s18rscvibvm91zw0kkq7ylrhisf8vp8hkp6i")))) + "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) (build-system python-build-system) (arguments `(#:phases @@ -1774,15 +1774,14 @@ collections of DNA motifs.") (define-public clustal-omega (package (name "clustal-omega") - (version "1.2.1") + (version "1.2.4") (source (origin (method url-fetch) - (uri (string-append - "http://www.clustal.org/omega/clustal-omega-" - version ".tar.gz")) + (uri (string-append "http://www.clustal.org/omega/clustal-omega-" + version ".tar.gz")) (sha256 (base32 - "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf")))) + "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6")))) (build-system gnu-build-system) (inputs `(("argtable" ,argtable))) @@ -4890,6 +4889,43 @@ subsequent visualization, annotation and storage of results.") ;; LGPLv2.1+ (license (list license:gpl2 license:lgpl2.1+)))) +(define-public plink-ng + (package (inherit plink) + (name "plink-ng") + (version "1.90b4") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/chrchang/plink-ng/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:make-flags (list "BLASFLAGS=-llapack -lopenblas" + "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" + "ZLIB=-lz" + "-f" "Makefile.std") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "1.9") #t)) + (delete 'configure) ; no "configure" script + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin/"))) + (install-file "plink" bin) + #t)))))) + (inputs + `(("zlib" ,zlib) + ("lapack" ,lapack) + ("openblas" ,openblas))) + (home-page "https://www.cog-genomics.org/plink/") + (license license:gpl3+))) + (define-public smithlab-cpp (let ((revision "1") (commit "728a097bec88c6f4b8528b685932049e660eff2e")) @@ -8070,7 +8106,7 @@ library implementing most of the pipeline's features.") (define-public rcas-web (package (name "rcas-web") - (version "0.0.3") + (version "0.0.4") (source (origin (method url-fetch) @@ -8079,7 +8115,7 @@ library implementing most of the pipeline's features.") "/rcas-web-" version ".tar.gz")) (sha256 (base32 - "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq")))) + "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm")))) (build-system gnu-build-system) (arguments `(#:phases @@ -9977,7 +10013,7 @@ browser.") (revision "1")) (package (name "f-seq") - (version (string-append "1.1-" revision "." commit)) + (version (string-append "1.1-" revision "." (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -10086,3 +10122,51 @@ straight away. Its main features are: and CHH context @end itemize\n") (license license:gpl3+))) + +(define-public paml + (package + (name "paml") + (version "4.9e") + (source (origin + (method url-fetch) + (uri (string-append "http://abacus.gene.ucl.ac.uk/software/" + "paml" version ".tgz")) + (sha256 + (base32 + "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6")) + (modules '((guix build utils))) + ;; Remove Windows binaries + (snippet + '(begin + (for-each delete-file (find-files "." "\\.exe$")) + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "src/BFdriver.c" + (("/bin/bash") (which "bash"))) + (chdir "src") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((tools '("baseml" "basemlg" "codeml" + "pamp" "evolver" "yn00" "chi2")) + (bin (string-append (assoc-ref outputs "out") "/bin")) + (docdir (string-append (assoc-ref outputs "out") + "/share/doc/paml"))) + (mkdir-p bin) + (for-each (lambda (file) (install-file file bin)) tools) + (copy-recursively "../doc" docdir) + #t)))))) + (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html") + (synopsis "Phylogentic analysis by maximum likelihood") + (description "PAML (for Phylogentic Analysis by Maximum Likelihood) +contains a few programs for model fitting and phylogenetic tree reconstruction +using nucleotide or amino-acid sequence data.") + ;; GPLv3 only + (license license:gpl3))) |