From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Guix-devel <guix-devel@gnu.org>
Subject: [PATCH]: gnu: Add HISAT.
Date: Mon, 9 Feb 2015 12:16:19 +0100 [thread overview]
Message-ID: <idjlhk772t8.fsf@bimsb-sys02.mdc-berlin.net> (raw)
[-- Attachment #1: Type: text/plain, Size: 272 bytes --]
Attached is a patch to add HISAT, another popular read aligner.
I would have really liked to use snippets here for a few static changes
to the sources, but it seems that snippets cannot be used with zip
archives (see my earlier message to the mailing list).
~~ Ricardo
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-HISAT.patch --]
[-- Type: text/x-patch, Size: 4284 bytes --]
From 305768bfef9bf4bc8d57828e27b8439dedd574bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 9 Feb 2015 12:13:26 +0100
Subject: [PATCH] gnu: Add HISAT.
* gnu/packages/bioinformatics.scm (hisat): New variable.
---
gnu/packages/bioinformatics.scm | 77 ++++++++++++++++++++++++++++++++++++++++-
1 file changed, 76 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c0d1438..425558d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -29,8 +29,9 @@
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
- #:use-module (gnu packages python))
+ #:use-module (gnu packages python)
#:use-module (gnu packages tbb)
+ #:use-module (gnu packages zip))
(define-public bedtools
(package
@@ -181,6 +182,80 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
+(define-public hisat
+ (package
+ (name "hisat")
+ (version "0.1.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
+ version "-beta-source.zip"))
+ (sha256
+ (base32
+ "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no check target
+ #:make-flags '("allall")
+ #:phases
+ (alist-replace
+ 'unpack
+ (lambda* (#:key source #:allow-other-keys)
+ (and (zero? (system* "unzip" source))
+ (chdir "hisat-0.1.4-beta")))
+ (alist-cons-after
+ 'unpack 'patch-sources
+ (lambda _
+ ;; XXX Cannot use snippet because zip files are not supported
+ (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\\\"\""))
+ (substitute* '("hisat-build" "hisat-inspect")
+ (("/usr/bin/env") (which "env"))))
+ (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)))
+ '("hisat"
+ "hisat-build"
+ "hisat-build-s"
+ "hisat-build-l"
+ "hisat-align-s"
+ "hisat-align-l"
+ "hisat-inspect"
+ "hisat-inspect-s"
+ "hisat-inspect-l"
+ "hisat-build-s-debug"
+ "hisat-build-l-debug"
+ "hisat-align-s-debug"
+ "hisat-align-l-debug"
+ "hisat-inspect-s-debug"
+ "hisat-inspect-l-debug"))))
+ (alist-delete 'configure %standard-phases))))))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (inputs
+ `(("perl" ,perl)
+ ("python" ,python)
+ ("zlib" ,zlib)))
+ (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
+ (synopsis "Hierarchical indexing for spliced alignment of transcripts")
+ (description
+ "HISAT is a fast and sensitive spliced alignment program for mapping
+RNA-seq reads. In addition to one global FM index that represents a whole
+genome, HISAT uses a large set of small FM indexes that collectively cover the
+whole genome. These small indexes (called local indexes) combined with
+several alignment strategies enable effective alignment of RNA-seq reads, in
+particular, reads spanning multiple exons.")
+ (license license:gpl3)))
+
(define-public samtools
(package
(name "samtools")
--
2.1.0
next reply other threads:[~2015-02-09 11:16 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-02-09 11:16 Ricardo Wurmus [this message]
2015-02-09 23:03 ` [PATCH]: gnu: Add HISAT Ludovic Courtès
2015-02-10 9:42 ` Ricardo Wurmus
2015-02-10 10:24 ` Ricardo Wurmus
2015-02-10 12:52 ` Ludovic Courtès
2015-02-11 11:15 ` Andreas Enge
2015-02-11 16:14 ` Ricardo Wurmus
2015-02-11 16:23 ` Andreas Enge
2015-02-11 22:40 ` Ludovic Courtès
2015-02-12 11:04 ` Ricardo Wurmus
2015-02-12 12:51 ` Andreas Enge
2015-02-12 20:39 ` Ludovic Courtès
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=idjlhk772t8.fsf@bimsb-sys02.mdc-berlin.net \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).