diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 229 |
1 files changed, 114 insertions, 115 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index ed6d4d4..397b38f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1601,7 +1601,7 @@ runApp(launch.browser=0, port=4208)~%\n" (define-public seqwish (package (name "seqwish") - (version "0.7.9") + (version "0.7.11") (source (origin (method git-fetch) (uri (git-reference @@ -1610,7 +1610,7 @@ runApp(launch.browser=0, port=4208)~%\n" (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x")) + (base32 "18wsrvqf0nsfk29v3ggdq2r4q15d4n4sq8v228qq1jsybbjlkgsa")) (patches (search-patches "seqwish-paryfor-riscv.diff" "seqwish-shared-library.diff")) (snippet @@ -1810,14 +1810,14 @@ dictionaries to record a queryable version of the graph.") (define-public smoothxg (package (name "smoothxg") - (version "0.7.2") + (version "0.8.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/pangenome/smoothxg" "/releases/download/v" version "/smoothxg-v" version ".tar.gz")) (sha256 - (base32 "1px8b5aaa23z85i7ximdamk2jj7wk5hb7bpbrgxsvkxc69zlwy38")) + (base32 "1gl4dskj81hlma7wsjrwwg77hgzk7dc9iaqqnf2wzrf2f4ll1cdj")) (snippet #~(begin (use-modules (guix build utils)) @@ -1855,7 +1855,8 @@ dictionaries to record a queryable version of the graph.") (with-directory-excursion (string-append "../smoothxg-v" #$version "/deps/abPOA") (substitute* "Makefile" - (("-march=native") "")) + (("-march=native") "") + (("-march=armv8-a\\+simd") "")) (apply invoke "make" "libabpoa" make-flags))))))) (inputs (list jemalloc @@ -1897,14 +1898,14 @@ The path-guided stochastic gradient descent based 1D sort implemented in (define-public graphaligner (package (name "graphaligner") - (version "1.0.14") + (version "1.0.19") (source (origin (method url-fetch) (uri (string-append "https://github.com/maickrau/GraphAligner/files/" - "7813545/GraphAligner.tar.gz")) + "14037134/GraphAligner.tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1y4vwp03fl2ck6bnyn0sc97vgvdb8i0yfzjk5mv5gk0bc7a4f0n1")))) + (base32 "1z1rxvl2pmiqbh670phkx7vma36w90ylp27wyadlbzf32pa2cpdn")))) (build-system gnu-build-system) (arguments (list @@ -1938,17 +1939,18 @@ The path-guided stochastic gradient descent based 1D sort implemented in (install-file header (string-append out "/include"))) (find-files "src" "\\.h(pp)?$")))))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("sparsehash" ,sparsehash))) + (list (list jemalloc "bin") + pkg-config + sparsehash)) (inputs - `(("boost" ,boost) - ("concurrentqueue" ,concurrentqueue) - ("jemalloc" ,jemalloc) - ("libdivsufsort" ,libdivsufsort) - ("mummer" ,mummer) - ("protobuf" ,protobuf) - ("sdsl-lite" ,sdsl-lite) - ("zlib" ,zlib))) + (list boost + concurrentqueue + jemalloc + libdivsufsort + mummer + protobuf + sdsl-lite + zlib)) (home-page "https://github.com/maickrau/GraphAligner") (synopsis "Seed-and-extend program for aligning genome graphs") (description "Seed-and-extend program for aligning long error-prone reads to @@ -2141,7 +2143,7 @@ suitable for long reads, but works also well with short reads.") (define-public odgi (package (name "odgi") - (version "0.8.3") + (version "0.9.0") (outputs '("out" "static")) (source (origin (method url-fetch) @@ -2149,7 +2151,7 @@ suitable for long reads, but works also well with short reads.") "/download/v" version "/odgi-v" version ".tar.gz")) (sha256 - (base32 "1gw1xdb945z25rar6pba6kq5xdx8l7fkhxjyrvc1z1brva53p9hk")) + (base32 "0brg0sz45v1wv4ld3p4jwiab10nyp2f691zfwpiva6g6f71q3cbk")) (snippet #~(begin (use-modules (guix build utils)) @@ -3548,36 +3550,37 @@ protein alignments and syntenic genomic alignments.") (define-public pplacer (let ((commit "807f6f3")) - (build-with-ocaml4.07 - (package - (name "pplacer") - ;; The commit should be updated with each version change. - (version "1.1.alpha19") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/matsen/pplacer") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) - (build-system ocaml-build-system) - (arguments - `(#:modules ((guix build ocaml-build-system) - (guix build utils) - (ice-9 ftw)) + (build-with-ocaml4.07 + (package + (name "pplacer") + ;; The commit should be updated with each version change. + (version "1.1.alpha19") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/matsen/pplacer") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) + (build-system ocaml-build-system) + (arguments + (list + #:modules '((guix build ocaml-build-system) + (guix build utils) + (ice-9 ftw)) #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'fix-build-with-latest-ocaml - (lambda _ - (substitute* "myocamlbuild.ml" - (("dep \\[\"c_pam\"\\]" m) - (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n" - m)) - (("let run_and_read" m) - (string-append " + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-build-with-latest-ocaml + (lambda _ + (substitute* "myocamlbuild.ml" + (("dep \\[\"c_pam\"\\]" m) + (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n" + m)) + (("let run_and_read" m) + (string-append " let split s ch = let x = ref [] in let rec go s = @@ -3593,76 +3596,72 @@ let before_space s = with Not_found -> s " m)) - (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m) - (string-append "List.map before_space (split_nl & " m ")")) - ((" blank_sep_strings &") "") - ((" Lexing.from_string &") "")) - #t)) - (add-after 'unpack 'replace-bundled-cddlib - (lambda* (#:key inputs #:allow-other-keys) - (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) - (local-dir "cddlib_guix")) - (mkdir local-dir) - (with-directory-excursion local-dir - (invoke "tar" "xvf" cddlib-src)) - (let ((cddlib-src-folder - (string-append local-dir "/" - (list-ref (scandir local-dir) 2) - "/lib-src"))) - (for-each make-file-writable (find-files "cdd_src" ".*")) - (for-each - (lambda (file) - (copy-file file - (string-append "cdd_src/" (basename file)))) - (find-files cddlib-src-folder ".*[ch]$"))) - #t))) - (add-after 'unpack 'fix-makefile - (lambda _ - ;; Remove system calls to 'git'. - (substitute* "Makefile" - (("^DESCRIPT:=pplacer-.*") - (string-append - "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) - (substitute* "myocamlbuild.ml" - (("git describe --tags --long .*\\\" with") - (string-append - "echo -n v" ,version "-" ,commit "\" with"))) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (copy-recursively "bin" bin)) - #t))) - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib)) - (inputs - `(("zlib" ,zlib "static") - ("gsl" ,gsl-static) - ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit)) - ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries)) - ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip)) - ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv)) - ("ocaml-sqlite3" ,(package-with-ocaml4.07 ocaml-sqlite3)) - ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm)) - ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl)) - ("ocaml-gsl" ,ocaml4.07-gsl-1) - ("sqlite:static" ,sqlite "static"))) - (native-inputs - `(("cddlib-src" ,(package-source cddlib)) - ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)) - ("pkg-config" ,pkg-config))) - (propagated-inputs - (list pplacer-scripts)) - (synopsis "Phylogenetic placement of biological sequences") - (description - "Pplacer places query sequences on a fixed reference phylogenetic tree + (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m) + (string-append "List.map before_space (split_nl & " m ")")) + ((" blank_sep_strings &") "") + ((" Lexing.from_string &") "")))) + (add-after 'unpack 'replace-bundled-cddlib + (lambda* (#:key inputs #:allow-other-keys) + (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) + (local-dir "cddlib_guix")) + (mkdir local-dir) + (with-directory-excursion local-dir + (invoke "tar" "xvf" cddlib-src)) + (let ((cddlib-src-folder + (string-append local-dir "/" + (list-ref (scandir local-dir) 2) + "/lib-src"))) + (for-each make-file-writable (find-files "cdd_src" ".*")) + (for-each + (lambda (file) + (copy-file file + (string-append "cdd_src/" (basename file)))) + (find-files cddlib-src-folder ".*[ch]$")))))) + (add-after 'unpack 'fix-makefile + (lambda _ + ;; Remove system calls to 'git'. + (substitute* "Makefile" + (("^DESCRIPT:=pplacer-.*") + (string-append + "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) + (substitute* "myocamlbuild.ml" + (("git describe --tags --long .*\\\" with") + (string-append + "echo -n v" ,version "-" ,commit "\" with"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (copy-recursively "bin" bin))))) + #:ocaml ocaml-4.07 + #:findlib ocaml4.07-findlib)) + (inputs + (list (list zlib "static") + (list gsl "static") + (package-with-ocaml4.07 ocaml-ounit) + (package-with-ocaml4.07 ocaml-batteries) + (package-with-ocaml4.07 camlzip) + (package-with-ocaml4.07 ocaml-csv) + (package-with-ocaml4.07 ocaml-sqlite3) + (package-with-ocaml4.07 ocaml-xmlm) + (package-with-ocaml4.07 ocaml-mcl) + ocaml4.07-gsl-1 + (list sqlite "static"))) + (native-inputs + (list (package-source cddlib) + (package-with-ocaml4.07 ocamlbuild) + pkg-config)) + (propagated-inputs + (list pplacer-scripts)) + (synopsis "Phylogenetic placement of biological sequences") + (description + "Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.") - (home-page "https://matsen.fhcrc.org/pplacer/") - (license license:gpl3))))) + (home-page "https://matsen.fhcrc.org/pplacer/") + (license license:gpl3))))) (define-public python2-biopython (python2-package python-biopython)) |