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-rw-r--r--gn/packages/bioinformatics.scm187
1 files changed, 92 insertions, 95 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 827fb3f..13bb00e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -3550,36 +3550,37 @@ protein alignments and syntenic genomic alignments.")
(define-public pplacer
(let ((commit "807f6f3"))
- (build-with-ocaml4.07
- (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))
+ (build-with-ocaml4.07
+ (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
+ (list
+ #: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 "
+ #~(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 =
@@ -3595,76 +3596,72 @@ let before_space 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
+ (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m)
+ (string-append "List.map before_space (split_nl & " m ")"))
+ ((" blank_sep_strings &") "")
+ ((" Lexing.from_string &") ""))))
+ (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]$"))))))
+ (add-after 'unpack 'fix-makefile
+ (lambda _
+ ;; Remove system calls to 'git'.
+ (substitute* "Makefile"
+ (("^DESCRIPT:=pplacer-.*")
+ (string-append
+ "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
+ (substitute* "myocamlbuild.ml"
+ (("git describe --tags --long .*\\\" with")
+ (string-append
+ "echo -n v" ,version "-" ,commit "\" with")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (copy-recursively "bin" bin)))))
+ #:ocaml ocaml-4.07
+ #:findlib ocaml4.07-findlib))
+ (inputs
+ (list (list zlib "static")
+ gsl-static
+ (package-with-ocaml4.07 ocaml-ounit)
+ (package-with-ocaml4.07 ocaml-batteries)
+ (package-with-ocaml4.07 camlzip)
+ (package-with-ocaml4.07 ocaml-csv)
+ (package-with-ocaml4.07 ocaml-sqlite3)
+ (package-with-ocaml4.07 ocaml-xmlm)
+ (package-with-ocaml4.07 ocaml-mcl)
+ ocaml4.07-gsl-1
+ (list sqlite "static")))
+ (native-inputs
+ (list (package-source cddlib)
+ (package-with-ocaml4.07 ocamlbuild)
+ 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)))))
+ (home-page "https://matsen.fhcrc.org/pplacer/")
+ (license license:gpl3)))))
(define-public python2-biopython
(python2-package python-biopython))
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-30 22:11:35 +0000