From b65c02e2d35af6fbe1d1810d6c69cfab194e13e2 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 6 Jun 2021 12:07:01 +0300
Subject: gnu: freebayes: Update to 1.3.5.

* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/packages/bioinformatics.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2de8a59d3c..1e38c6e0e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13572,7 +13572,7 @@ manipulations on VCF files.")
 (define-public freebayes
   (package
     (name "freebayes")
-    (version "1.3.3")
+    (version "1.3.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -13580,8 +13580,7 @@ manipulations on VCF files.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8"))
-              (patches (search-patches "freebayes-devendor-deps.patch"))
+               (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -13593,8 +13592,7 @@ manipulations on VCF files.")
        ("htslib" ,htslib)
        ("smithwaterman" ,smithwaterman)
        ("tabixpp" ,tabixpp)
-       ("vcflib" ,vcflib)
-       ("zlib" ,zlib)))
+       ("vcflib" ,vcflib)))
     (native-inputs
      `(("bash-tap" ,bash-tap)
        ("bc" ,bc)
@@ -13627,13 +13625,13 @@ manipulations on VCF files.")
                   (string-append bash-tap "/bin/bash-tap-bootstrap"))
                  (("source.*bash-tap-bootstrap")
                   (string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
-               (substitute* "meson.build"
-                  ;; Some inputs aren't actually needed.
-                 ((".*bamtools/src.*") "")
-                 ((".*multichoose.*") ""))
                (substitute* '("src/BedReader.cpp"
                               "src/BedReader.h")
                  (("../intervaltree/IntervalTree.h") "IntervalTree.h"))
+               (substitute* "meson.build"
+                 ;; Our pkg-config file is vcflib.pc
+                 (("libvcflib") "vcflib")
+                 (("vcflib_inc,") ""))
                #t)))
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs #:allow-other-keys)
-- 
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