01/03: gnu: bowtie: Update to 2.2.6.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 0047d26a220805a99c84d9b87c73e012a63919e1
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Jan 14 14:36:32 2016 +0100

    gnu: bowtie: Update to 2.2.6.
    
    * gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
    [source]: Remove patch; do not set CC and CPP variables.
    [inputs]: Add "tbb".
    [arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
    "install" phase.
    * gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
    * gnu-system.am (dist_patch_DATA): Remove patch file.
---
 gnu-system.am                                  |    1 -
 gnu/packages/bioinformatics.scm                |   38 ++++++++++--------------
 gnu/packages/patches/bowtie-fix-makefile.patch |   31 -------------------
 3 files changed, 16 insertions(+), 54 deletions(-)

diff --git a/gnu-system.am b/gnu-system.am
index fa2f038..dc2631b 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -416,7 +416,6 @@ dist_patch_DATA =                                           
\
   gnu/packages/patches/avidemux-install-to-lib.patch           \
   gnu/packages/patches/avrdude-fix-libusb.patch                        \
   gnu/packages/patches/bash-completion-directories.patch       \
-  gnu/packages/patches/bowtie-fix-makefile.patch               \
   gnu/packages/patches/bigloo-gc-shebangs.patch                        \
   gnu/packages/patches/binutils-ld-new-dtags.patch             \
   gnu/packages/patches/binutils-loongson-workaround.patch      \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a0b7864..50e1ce7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ricardo Wurmus <address@hidden>
+;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <address@hidden>
 ;;; Copyright © 2015, 2016 Ben Woodcroft <address@hidden>
 ;;; Copyright © 2015 Pjotr Prins <address@hidden>
 ;;; Copyright © 2015 Andreas Enge <address@hidden>
@@ -603,7 +603,7 @@ errors at the end of reads.")
 (define-public bowtie
   (package
     (name "bowtie")
-    (version "2.2.4")
+    (version "2.2.6")
     (source (origin
               (method url-fetch)
               (uri (string-append 
"https://github.com/BenLangmead/bowtie2/archive/v";
@@ -611,42 +611,36 @@ errors at the end of reads.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
+                "1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86"))
               (modules '((guix build utils)))
               (snippet
                '(substitute* "Makefile"
-                  (("^CC = .*$") "CC = gcc")
-                  (("^CPP = .*$") "CPP = g++")
                   ;; replace BUILD_HOST and BUILD_TIME for deterministic build
                   (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
-                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
-              (patches (list (search-patch "bowtie-fix-makefile.patch")))))
+                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
     (build-system gnu-build-system)
     (inputs `(("perl" ,perl)
               ("perl-clone" ,perl-clone)
               ("perl-test-deep" ,perl-test-deep)
               ("perl-test-simple" ,perl-test-simple)
-              ("python" ,python-2)))
+              ("python" ,python-2)
+              ("tbb" ,tbb)))
     (arguments
-     '(#:make-flags '("allall")
+     '(#:make-flags
+       (list "allall"
+             "WITH_TBB=1"
+             (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (alist-delete
         'configure
         (alist-replace
-         'install
+         'check
          (lambda* (#:key outputs #:allow-other-keys)
-           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
-             (for-each (lambda (file)
-                         (install-file file bin))
-                       (find-files "." "bowtie2.*"))))
-         (alist-replace
-          'check
-          (lambda* (#:key outputs #:allow-other-keys)
-            (system* "perl"
-                     "scripts/test/simple_tests.pl"
-                     "--bowtie2=./bowtie2"
-                     "--bowtie2-build=./bowtie2-build"))
-          %standard-phases)))))
+           (system* "perl"
+                    "scripts/test/simple_tests.pl"
+                    "--bowtie2=./bowtie2"
+                    "--bowtie2-build=./bowtie2-build"))
+         %standard-phases))))
     (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml";)
     (synopsis "Fast and sensitive nucleotide sequence read aligner")
     (description
diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch 
b/gnu/packages/patches/bowtie-fix-makefile.patch
deleted file mode 100644
index 5ac6573..0000000
--- a/gnu/packages/patches/bowtie-fix-makefile.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001
-From: Valentin Antonescu <address@hidden>
-Date: Tue, 2 Dec 2014 11:19:13 -0500
-Subject: [PATCH] Make sure the Mavericks test happens only under Darwin.
-
----
- Makefile | 11 +++++------
- 1 file changed, 5 insertions(+), 6 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index d74f7c8..a4cdfa7 100644
---- a/Makefile
-+++ b/Makefile
-@@ -54,12 +54,11 @@ endif
- MACOS = 0
- ifneq (,$(findstring Darwin,$(shell uname)))
-       MACOS = 1
--endif
--
--ifneq (,$(findstring 13,$(shell uname -r)))
--      CPP = clang++
--      CC = clang
--      EXTRA_FLAGS += -stdlib=libstdc++
-+      ifneq (,$(findstring 13,$(shell uname -r)))
-+              CPP = clang++
-+              CC = clang
-+              EXTRA_FLAGS += -stdlib=libstdc++
-+      endif
- endif
- 
- POPCNT_CAPABILITY ?= 1