From d397cb6207ab96d476d4ea8880a675b67f429bf5 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Tue, 31 May 2022 14:19:46 -0400
Subject: gnu: Remove pplacer.

* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
---
 gnu/packages/bioinformatics.scm | 117 ----------------------------------------
 1 file changed, 117 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b92a0b5829..64e4171f8f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13245,123 +13245,6 @@ Additionally, the AdapterRemoval may be used to recover a consensus adapter
 sequence for paired-ended data, for which this information is not available.")
     (license license:gpl3+)))
 
-(define-public pplacer
-  (let ((commit "807f6f3"))
-    (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))
-         #: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 "
-let split s ch =
-  let x = ref [] in
-  let rec go s =
-    let pos = String.index s ch in
-    x := (String.before s pos)::!x;
-    go (String.after s (pos + 1))
-  in
-  try go s
-  with Not_found -> !x
-let split_nl s = split s '\\n'
-let before_space s =
-  try String.before s (String.index 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
-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))))
-
 ;; 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.
-- 
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