diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 125 |
1 files changed, 125 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36b9087e4a..6ef8690e48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -33,6 +33,7 @@ #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix build-system r) @@ -71,6 +72,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) + #:use-module (gnu packages ocaml) #:use-module (gnu packages pcre) #:use-module (gnu packages parallel) #:use-module (gnu packages pdf) @@ -3627,6 +3629,129 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (home-page "https://github.com/wwood/OrfM") (license license:lgpl3+))) +(define-public pplacer + (let ((commit "g807f6f3")) + (package + (name "pplacer") + ;; The commit should be updated with each version change. + (version "1.1.alpha19") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/matsen/pplacer/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) + (build-system ocaml-build-system) + (arguments + `(#:ocaml ,ocaml-4.01 + #:findlib ,ocaml4.01-findlib + #:modules ((guix build ocaml-build-system) + (guix build utils) + (ice-9 ftw)) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (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 + (system* "tar" "xvf" cddlib-src)) + (let ((cddlib-src-folder + (string-append local-dir "/" + (list-ref (scandir local-dir) 2) + "/lib-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))))) + (native-inputs + `(("zlib" ,zlib) + ("gsl" ,gsl) + ("ocaml-ounit" ,ocaml4.01-ounit) + ("ocaml-batteries" ,ocaml4.01-batteries) + ("ocaml-camlzip" ,ocaml4.01-camlzip) + ("ocaml-csv" ,ocaml4.01-csv) + ("ocaml-sqlite3" ,ocaml4.01-sqlite3) + ("ocaml-xmlm" ,ocaml4.01-xmlm) + ("ocaml-mcl" ,ocaml4.01-mcl) + ("ocaml-gsl" ,ocaml4.01-gsl) + ("cddlib-src" ,(package-source cddlib)))) + (propagated-inputs + `(("pplacer-scripts" ,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 "http://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"))) + (replace 'check + (lambda _ + (zero? (system* "python" "-m" "unittest" "discover" "-v")))) + (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 python2-pbcore (package (name "python2-pbcore") |