1 files changed, 125 insertions(+), 0 deletions(-)

M 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")