diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 157 |
1 files changed, 157 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 3dc3898..87242ed 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -14,6 +14,7 @@ #:use-module (guix build-system copy) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) + #:use-module (guix build-system ocaml) #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (guix build-system waf) @@ -2638,6 +2639,162 @@ protein alignments and syntenic genomic alignments.") "https://opensource.org/licenses/artistic-license-1.0" "Artistic-license-1.0")))) +(define-public pplacer + (let ((commit "807f6f3")) + (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)) + #: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 " +let split s ch = + let x = ref [] in + let rec go s = + let pos = String.index s ch in + x := (String.before s pos)::!x; + go (String.after s (pos + 1)) + in + try go s + with Not_found -> !x +let split_nl s = split s '\\n' +let before_space s = + try String.before s (String.index 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 +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)))) + +;; This package is installed alongside 'pplacer'. It is a separate package so +;; that it can use the python-build-system for the scripts that are +;; distributed alongside the main OCaml binaries. +(define pplacer-scripts + (package + (inherit pplacer) + (name "pplacer-scripts") + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-scripts-dir + (lambda _ (chdir "scripts") #t)) + (replace 'check + (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) + (add-after 'install 'wrap-executables + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (let ((path (string-append + (assoc-ref inputs "hmmer") "/bin:" + (assoc-ref inputs "infernal") "/bin"))) + (display path) + (wrap-program (string-append bin "/refpkg_align.py") + `("PATH" ":" prefix (,path)))) + (let ((path (string-append + (assoc-ref inputs "hmmer") "/bin"))) + (wrap-program (string-append bin "/hrefpkg_query.py") + `("PATH" ":" prefix (,path))))) + #t))))) + (inputs + `(("infernal" ,infernal) + ("hmmer" ,hmmer))) + (propagated-inputs + `(("python-biopython" ,python2-biopython) + ("taxtastic" ,taxtastic))) + (synopsis "Pplacer Python scripts"))) + (define-public sepp (package (name "sepp") |