01/02: gnu: minimap2: Update to 2.18.

[guix-commits]

efraim pushed a commit to branch master
in repository guix.

commit 36a90d0637bb47b113ceda5abb64c50600837436
Author: Efraim Flashner <efraim@flashner.co.il>
AuthorDate: Wed May 26 13:40:59 2021 +0300

    gnu: minimap2: Update to 2.18.
    
    * gnu/packages/bioinformatics.scm (minimap2): Update to 2.18.
    [source]: Remove patch.
    * gnu/packages/patches/minimap2-aarch64-support.patch: Remove file.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    |  5 +--
 .../patches/minimap2-aarch64-support.patch         | 52 ----------------------
 3 files changed, 2 insertions(+), 56 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index b0df9d5..8355a20 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1424,7 +1424,6 @@ dist_patch_DATA =                                         
\
   %D%/packages/patches/mingw-w64-6.0.0-gcc.patch               \
   %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch     \
   %D%/packages/patches/mingw-w64-reproducible-gendef.patch     \
-  %D%/packages/patches/minimap2-aarch64-support.patch          \
   %D%/packages/patches/minisat-friend-declaration.patch                \
   %D%/packages/patches/minisat-install.patch                   \
   %D%/packages/patches/mit-krb5-hurd.patch                     \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 074ff80..46092fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12323,7 +12323,7 @@ version does count multisplits.")
 (define-public minimap2
   (package
     (name "minimap2")
-    (version "2.17")
+    (version "2.18")
     (source
      (origin
        (method url-fetch)
@@ -12332,8 +12332,7 @@ version does count multisplits.")
                            "minimap2-" version ".tar.bz2"))
        (sha256
         (base32
-         "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))
-       (patches (search-patches "minimap2-aarch64-support.patch"))))
+         "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are none
diff --git a/gnu/packages/patches/minimap2-aarch64-support.patch 
b/gnu/packages/patches/minimap2-aarch64-support.patch
deleted file mode 100644
index 95db857..0000000
--- a/gnu/packages/patches/minimap2-aarch64-support.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-This patch should be removed with the next release. There is WIP upstream
-support for proper support of more architectures, including aarch64 and 
powerpc64le.
-
-diff --git a/Makefile b/Makefile
-index ed341f6..94dbd85 100644
---- a/Makefile
-+++ b/Makefile
-@@ -6,20 +6,18 @@ PROG=                minimap2
- PROG_EXTRA=   sdust minimap2-lite
- LIBS=         -lm -lz -lpthread
- 
--ifeq ($(arm_neon),) # if arm_neon is not defined
--ifeq ($(sse2only),) # if sse2only is not defined
--      OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o 
ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
--else                # if sse2only is defined
--      OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
--endif
--else                          # if arm_neon is defined
-+ifneq ($(arm_neon),)          # if arm_neon is defined
-       OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
--    INCLUDES+=-Isse2neon
--ifeq ($(aarch64),)    #if aarch64 is not defined
-       CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
--else                          #if aarch64 is defined
-+      INCLUDES+=-Isse2neon
-+else ifneq ($(aarch64),)      #if aarch64 is defined
-+      OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
-       CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
--endif
-+      INCLUDES+=-Isse2neon
-+else ifneq ($(sse2only),)     # if sse2only is defined
-+      OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
-+else                          # none of the above
-+      OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o 
ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
- endif
- 
- .PHONY:all extra clean depend
-@@ -46,9 +44,12 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h 
ketopt.h sdust.h
- 
- # SSE-specific targets on x86/x86_64
- 
--ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the 
default setting (i.e. no -msse2)
-+ifneq ($(arm_neon),)   # if arm_neon is defined, compile this target with the 
default setting (i.e. no -msse2)
-+ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
-+else ifneq ($(aarch64),)
- ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
--              $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
-+else
-+      $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
- endif
- 
- ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h