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-rw-r--r--gnu/packages/bioinformatics.scm125
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")