gnu: Add pplacer.
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
This commit is contained in:
Ben Woodcroft
parent
ad0ae297d4
commit
c033f5d6b5
1 changed files with 125 additions and 0 deletions
|
|
@ -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")
|
||||
|
|
|
|||
Reference in a new issue