From 4d7bb37981d5d1e639cbd7837cddc76c45271de2 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Thu, 12 May 2022 16:40:49 -0400
Subject: gnu: Remove fraggenescan.

* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
---
 gnu/packages/bioinformatics.scm | 90 -----------------------------------------
 1 file changed, 90 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9b30247594..3223d6eea8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3660,96 +3660,6 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
 Illumina, Roche 454, and the SOLiD platform.")
     (license license:bsd-3)))
 
-(define-public fraggenescan
-  (package
-    (name "fraggenescan")
-    (version "1.30")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "mirror://sourceforge/fraggenescan/"
-                       "FragGeneScan" version ".tar.gz"))
-       (sha256
-        (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (add-before 'build 'patch-paths
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (string-append (assoc-ref outputs "out")))
-                    (share (string-append out "/share/fraggenescan/")))
-               (substitute* "run_FragGeneScan.pl"
-                 (("system\\(\"rm")
-                  (string-append "system(\"" (which "rm")))
-                 (("system\\(\"mv")
-                  (string-append "system(\"" (which "mv")))
-                 (("\\\"awk") (string-append "\"" (which "awk")))
-                 ;; This script and other programs expect the training files
-                 ;; to be in the non-standard location bin/train/XXX. Change
-                 ;; this to be share/fraggenescan/train/XXX instead.
-                 (("^\\$train.file = \\$dir.*")
-                  (string-append "$train_file = \""
-                                 share
-                                 "train/\".$FGS_train_file;")))
-               (substitute* "run_hmm.c"
-                 (("^  strcat\\(train_dir, \\\"train/\\\"\\);")
-                  (string-append "  strcpy(train_dir, \"" share "/train/\");"))))
-             #t))
-         (replace 'build
-           (lambda _
-             (invoke "make" "clean")
-             (invoke "make" "fgs")
-             #t))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (string-append (assoc-ref outputs "out")))
-                    (bin (string-append out "/bin/"))
-                    (share (string-append out "/share/fraggenescan/train")))
-               (install-file "run_FragGeneScan.pl" bin)
-               (install-file "FragGeneScan" bin)
-               (copy-recursively "train" share))
-             #t))
-         (delete 'check)
-         (add-after 'install 'post-install-check
-           ;; In lieu of 'make check', run one of the examples and check the
-           ;; output files gets created.
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (string-append (assoc-ref outputs "out")))
-                    (bin (string-append out "/bin/"))
-                    (frag (string-append bin "run_FragGeneScan.pl")))
-               ;; Test complete genome.
-               (invoke frag
-                       "-genome=./example/NC_000913.fna"
-                       "-out=./test2"
-                       "-complete=1"
-                       "-train=complete")
-               (unless (and (file-exists? "test2.faa")
-                            (file-exists? "test2.ffn")
-                            (file-exists? "test2.gff")
-                            (file-exists? "test2.out"))
-                 (error "Expected files do not exist."))
-               ;; Test incomplete sequences.
-               (invoke frag
-                       "-genome=./example/NC_000913-fgs.ffn"
-                       "-out=out"
-                       "-complete=0"
-                       "-train=454_30")
-               #t))))))
-    (inputs
-     `(("perl" ,perl)
-       ("python" ,python-2))) ;not compatible with python 3.
-    (home-page "https://sourceforge.net/projects/fraggenescan/")
-    (synopsis "Finds potentially fragmented genes in short reads")
-    (description
-     "FragGeneScan is a program for predicting bacterial and archaeal genes in
-short and error-prone DNA sequencing reads.  It can also be applied to predict
-genes in incomplete assemblies or complete genomes.")
-    ;; GPL3+ according to private correspondense with the authors.
-    (license license:gpl3+)))
-
 (define-public fxtract
   (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
     (package
-- 
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