diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 187 |
1 files changed, 92 insertions, 95 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 827fb3f..13bb00e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -3550,36 +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 = @@ -3595,76 +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") + 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)) |