From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Diane Trout <diane@ghic.org>
Cc: guix-devel@gnu.org
Subject: [PATCH] Add BLESS (was: Re: Bioinformatics package: Bless)
Date: Fri, 6 Nov 2015 15:28:23 +0100 [thread overview]
Message-ID: <idjvb9f19tk.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <2238503.mBpvBuW9qZ@myrada>
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Hi,
> One of our users asked me to install a package "bless" that required a newer
> version of MPI than Debian provides, so I thought I'd try to build a guix
> package as Guix actually has openmpi 1.8 packaged.
Great! Thank you for your contribution.
> The source tarball has the GPL-3 LICENSE file, however it does also contain
> convenience copies of other source, and in my packaging I only spliced out one
> -- the pigz dependency.
I have taken your recipe and removed more bundled sources in a snippet.
There’s still bundled stuff that we should get rid of, most importantly
kmc, which brings its own executables.
I also changed the description based on the paper; instead of patching
the Makefile I overwrite the make flags.
Attached is a patch. Does this work for you?
What do others think about this patch?
~~ Ricardo
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From 11496448abe3717279d5b6a5d31eedae7a1dcc89 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 6 Nov 2015 15:22:26 +0100
Subject: [PATCH] gnu: Add BLESS.
* gnu/packages/bioinformatics.scm (bless): New variable.
---
gnu/packages/bioinformatics.scm | 83 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 83 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fbc1f4e..c28f833 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -44,6 +44,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -524,6 +525,88 @@ confidence to have in an alignment.")
license:lgpl2.0+
license:asl2.0))))
+(define-public bless
+ (package
+ (name "bless")
+ (version "1p02")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
+ version ".tgz"))
+ (sha256
+ (base32
+ "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
+ (modules '((guix build utils)))
+ (snippet
+ `(begin
+ ;; Remove bundled boost, pigz, zlib, and .git directory
+ ;; FIXME: also remove bundled sources for google-sparsehash,
+ ;; murmurhash3, kmc once packaged.
+ (delete-file-recursively "boost")
+ (delete-file-recursively "pigz")
+ (delete-file-recursively "zlib")
+ (delete-file-recursively ".git")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:make-flags
+ (list (string-append "ZLIB="
+ (assoc-ref %build-inputs "zlib")
+ "/lib/libz.a")
+ (string-append "LDFLAGS="
+ (string-join '("-lboost_filesystem"
+ "-lboost_system"
+ "-lboost_iostreams"
+ "-lz"
+ "-fopenmp"
+ "-std=c++11"))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-build-bundled-pigz
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("cd pigz/pigz-2.3.3; make") ""))
+ #t))
+ (add-after 'unpack 'patch-paths-to-executables
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "parse_args.cpp"
+ (("kmc_binary = .*")
+ (string-append "kmc_binary = \""
+ (assoc-ref outputs "out")
+ "/bin/kmc\";"))
+ (("pigz_binary = .*")
+ (string-append "pigz_binary = \""
+ (assoc-ref inputs "pigz")
+ "/bin/pigz\";")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ '("bless" "kmc/bin/kmc"))
+ #t)))
+ (delete 'configure))))
+ (native-inputs
+ `(("perl" ,perl)))
+ (inputs
+ `(("openmpi" ,openmpi)
+ ("boost" ,boost)
+ ("pigz" ,pigz)
+ ("zlib" ,zlib)))
+ (home-page "http://sourceforge.net/projects/bless-ec/wiki/Home/")
+ (synopsis "Bloom-filter-based error correction tool for NGS reads")
+ (description
+ "@dfn{Bloom-filter-based error correction solution for high-throughput
+sequencing reads} (BLESS) uses a single minimum-sized Bloo filter is a
+correction tool for genomic reads produced by @dfn{Next-generation
+sequencing} (NGS). BLESS produces accurate correction results with much less
+memory compared with previous solutions and is also able to tolerate a higher
+false-positive rate. BLESS can extend reads like DNA assemblers to correct
+errors at the end of reads.")
+ (license license:gpl3+)))
+
(define-public bowtie
(package
(name "bowtie")
--
2.1.0
next prev parent reply other threads:[~2015-11-06 14:28 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-11-05 19:49 Bioinformatics package: Bless Diane Trout
2015-11-06 14:28 ` Ricardo Wurmus [this message]
2015-11-06 15:12 ` [PATCH] Add BLESS Ludovic Courtès
2015-11-06 17:22 ` Ricardo Wurmus
2015-11-06 16:01 ` [PATCH] Add BLESS (was: Re: Bioinformatics package: Bless) Diane Trout
2015-11-06 19:14 ` [PATCH] Add BLESS Alex Kost
2015-11-06 20:03 ` Ricardo Wurmus
2015-11-06 21:16 ` Ludovic Courtès
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