From 4d93a9a36c3ddc431789fa38201b0fd657412dbe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 21 Oct 2018 23:03:57 +0200
Subject: gnu: seqan: Update to 2.4.0.

* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0.
[native-inputs]: Replace bzip2 with xz.
(seqan-1): New variable.
(tophat)[inputs]: Use seqan-1.
---
 gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++--------
 1 file changed, 47 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9163b5dc8a..cdb82aee8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1382,7 +1382,7 @@ gapped, local, and paired-end alignment modes.")
        ("python" ,python-2)
        ("perl" ,perl)
        ("zlib" ,zlib)
-       ("seqan" ,seqan)))
+       ("seqan" ,seqan-1)))
     (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
     (synopsis "Spliced read mapper for RNA-Seq data")
     (description
@@ -5733,14 +5733,15 @@ writing files into the .sra format.")
 (define-public seqan
   (package
     (name "seqan")
-    (version "1.4.2")
+    (version "2.4.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://packages.seqan.de/seqan-library/"
-                                  "seqan-library-" version ".tar.bz2"))
+              (uri (string-append "https://github.com/seqan/seqan/releases/"
+                                  "download/seqan-v" version
+                                  "/seqan-library-" version ".tar.xz"))
               (sha256
                (base32
-                "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
+                "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx"))))
     ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
     ;; makes sense to split the outputs.
     (outputs '("out" "doc"))
@@ -5750,11 +5751,11 @@ writing files into the .sra format.")
        #:builder
        (begin
          (use-modules (guix build utils))
-         (let ((tar  (assoc-ref %build-inputs "tar"))
-               (bzip (assoc-ref %build-inputs "bzip2"))
-               (out  (assoc-ref %outputs "out"))
-               (doc  (assoc-ref %outputs "doc")))
-           (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
+         (let ((tar (assoc-ref %build-inputs "tar"))
+               (xz  (assoc-ref %build-inputs "xz"))
+               (out (assoc-ref %outputs "out"))
+               (doc (assoc-ref %outputs "doc")))
+           (setenv "PATH" (string-append tar "/bin:" xz "/bin"))
            (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
            (chdir (string-append "seqan-library-" ,version))
            (copy-recursively "include" (string-append out "/include"))
@@ -5763,7 +5764,7 @@ writing files into the .sra format.")
     (native-inputs
      `(("source" ,source)
        ("tar" ,tar)
-       ("bzip2" ,bzip2)))
+       ("xz" ,xz)))
     (home-page "http://www.seqan.de")
     (synopsis "Library for nucleotide sequence analysis")
     (description
@@ -5774,6 +5775,41 @@ manipulation, online and indexed string search, efficient I/O of
 bioinformatics file formats, sequence alignment, and more.")
     (license license:bsd-3)))
 
+(define-public seqan-1
+  (package (inherit seqan)
+    (name "seqan")
+    (version "1.4.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://packages.seqan.de/seqan-library/"
+                                  "seqan-library-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
+    ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
+    ;; makes sense to split the outputs.
+    (outputs '("out" "doc"))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((tar  (assoc-ref %build-inputs "tar"))
+               (bzip (assoc-ref %build-inputs "bzip2"))
+               (out  (assoc-ref %outputs "out"))
+               (doc  (assoc-ref %outputs "doc")))
+           (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
+           (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+           (chdir (string-append "seqan-library-" ,version))
+           (copy-recursively "include" (string-append out "/include"))
+           (copy-recursively "share"  (string-append doc "/share"))
+           #t))))
+    (native-inputs
+     `(("source" ,source)
+       ("tar" ,tar)
+       ("bzip2" ,bzip2)))))
+
 (define-public seqmagick
   (package
     (name "seqmagick")
-- 
cgit v1.2.3