01/01: gnu: khmer: Update to 3.0.0a3.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit b556abe416a3e79b7f3b8cf491d8a3179c3d31c8
Author: Ricardo Wurmus <address@hidden>
Date:   Fri Jun 21 11:39:25 2019 +0200

    gnu: khmer: Update to 3.0.0a3.
    
    * gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3.
    [source]: Remove patch; remove seqan in snippet.
    [inputs]: Add seqan-1.
    * gnu/packages/patches/khmer-use-libraries.patch: Remove file.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                   |  1 -
 gnu/packages/bioinformatics.scm                | 12 +++++++++---
 gnu/packages/patches/khmer-use-libraries.patch | 16 ----------------
 3 files changed, 9 insertions(+), 20 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 4c54f02..a467501 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -951,7 +951,6 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch        \
   %D%/packages/patches/jbig2dec-ignore-testtest.patch          \
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch       \
-  %D%/packages/patches/khmer-use-libraries.patch                \
   %D%/packages/patches/libziparchive-add-includes.patch                \
   %D%/packages/patches/localed-xorg-keyboard.patch             \
   %D%/packages/patches/kiki-level-selection-crash.patch                \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f1a73bc..4f4d3d9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4168,7 +4168,7 @@ command, or queried for specific k-mers with 
@code{jellyfish query}.")
 (define-public khmer
   (package
     (name "khmer")
-    (version "2.1.2")
+    (version "3.0.0a3")
     (source
      (origin
        (method git-fetch)
@@ -4178,8 +4178,7 @@ command, or queried for specific k-mers with 
@code{jellyfish query}.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m"))
-       (patches (search-patches "khmer-use-libraries.patch"))
+         "01l4jczglkl7yfhgvzx8j0df7k54bk1r8sli9ll16i1mis0d8f37"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -4192,6 +4191,12 @@ command, or queried for specific k-mers with 
@code{jellyfish query}.")
            ;; 
https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
            (delete-file-recursively "third-party/zlib")
            (delete-file-recursively "third-party/bzip2")
+           (delete-file-recursively "third-party/seqan")
+           (substitute* "setup.cfg"
+             (("# libraries = z,bz2")
+              "libraries = z,bz2")
+             (("include:third-party/zlib:third-party/bzip2")
+              "include:"))
            #t))))
     (build-system python-build-system)
     (arguments
@@ -4208,6 +4213,7 @@ command, or queried for specific k-mers with 
@code{jellyfish query}.")
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
+       ("seqan" ,seqan-1)
        ("python-screed" ,python-screed)
        ("python-bz2file" ,python-bz2file)))
     (home-page "https://khmer.readthedocs.org/";)
diff --git a/gnu/packages/patches/khmer-use-libraries.patch 
b/gnu/packages/patches/khmer-use-libraries.patch
deleted file mode 100644
index 47d163a..0000000
--- a/gnu/packages/patches/khmer-use-libraries.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Change setup.cfg so that the bundled zlib and bzip2 are not used.  This cannot
-currently be achieved using "--library z,bz2" as instructed in the setup.py.
-
-diff --git a/setup.cfg b/setup.cfg
-index c054092..080992e 100644
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -1,7 +1,7 @@
- [build_ext]
- define = SEQAN_HAS_BZIP2,SEQAN_HAS_ZLIB
- undef = NO_UNIQUE_RC
--# libraries = z,bz2
-+libraries = z,bz2
- ## if using system libraries
- include-dirs = 
lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher
- # include-dirs = lib