>> + 'patch-makefile
>> + (lambda _
>> + (substitute* "Makefile"
>> + (("^CC = .*$") (string-append "CC = " (which "gcc")))
>> + (("^CPP = .*$") (string-append "CPP = " (which "g++")))
>> + ;; replace BUILD_HOST and BUILD_TIME for deterministic build
>> + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
>> + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
>
> Could you make this a ‘snippet’? It suffices to write “CC = gcc” and
> “CPP = g++”. That way, running ‘guix build -S bowtie’ will return
> source that’s closer to what we’re using.
Okay.
>> + (license license:gpl3)))
>
> From a quick glance, this should be ‘gpl3+’ (source file headers carry
> the “or any later version” phrase.)
I went by the NEWS and MANUAL files that say
"Bowtie 2 is licensed under the GPLv3 license."
and
"Bowtie 2 is distributed under the [GPLv3 license]"
but I have updated the package recipe to use `gpl3+' as the source file
headers do indeed carry the phrase "or any later version".
> Could you post an updated patch?
Please see the attached patch.
Thanks for the review!
Ricardo
PS: This depends on the Perl module "Clone" for which I sent a patch
previously. Although you said it was applied I haven't yet seen it in
the git repository.
>From 96f31057ba6bb17c1801f87d4bbae70dd3539576 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Tue, 16 Dec 2014 17:52:44 +0100
Subject: [PATCH] gnu: Add bowtie
* gnu/packages/bioinformatics.scm (bowtie): New variable.
---
gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a2846f1..ff6c337 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -77,6 +77,64 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:gpl2)))
+(define-public bowtie
+ (package
+ (name "bowtie")
+ (version "2.2.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v";
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
+ (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\\\"\"")))))
+ (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)))
+ (arguments
+ '(#:make-flags '("allall")
+ #:phases
+ (alist-delete
+ 'configure
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (copy-file file (string-append bin file)))
+ (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)))))
+ (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml";)
+ (synopsis "Fast and sensitive nucleotide sequence read aligner")
+ (description
+ "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
+reads to long reference sequences. It is particularly good at aligning reads
+of about 50 up to 100s or 1,000s of characters, and particularly good at
+aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
+genome with an FM Index to keep its memory footprint small: for the human
+genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
+gapped, local, and paired-end alignment modes.")
+ (license license:gpl3+)))
+
(define-public samtools
(package
(name "samtools")
--
1.9.3
