--- Begin Message ---
|
Subject: |
[PATCH] gnu: Add sambamba. |
|
Date: |
Mon, 6 Mar 2017 12:17:49 +0100 |
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
---
gnu/packages/bioinformatics.scm | 97 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 97 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7bf39c6b0..b6f753ef0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -63,6 +63,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
+ #:use-module (gnu packages ldc)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
@@ -8574,3 +8575,99 @@ identifications while not exceeding a specified false
discovery rate. It also
contains a number of utilities to explore the MS/MS results and assess missed
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
+
+(define htslib-for-sambamba
+ (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
+ (package
+ (inherit htslib)
+ (name "htslib-for-sambamba")
+ (version (string-append "1.3.1-1." (string-take commit 9)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lomereiter/htslib.git";)
+ (commit commit)))
+ (file-name (string-append "htslib-" version "-checkout"))
+ (sha256
+ (base32
+ "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments htslib)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'configure 'bootstrap
+ (lambda _
+ (zero? (system* "autoreconf" "-vif"))))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ,@(package-native-inputs htslib))))))
+
+(define-public sambamba
+ (package
+ (name "sambamba")
+ (version "0.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/lomereiter/sambamba/";
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there is no test target
+ #:make-flags
+ '("D_COMPILER=ldc2"
+ ;; Override "--compiler" flag only.
+ "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
+ "sambamba-ldmd2-64")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'place-biod
+ (lambda* (#:key inputs #:allow-other-keys)
+ (copy-recursively (assoc-ref inputs "biod") "BioD")
+ #t))
+ (add-after 'unpack 'unbundle-prerequisites
+ (lambda _
+ (substitute* "Makefile"
+ ((" htslib-static lz4-static") ""))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (install-file "build/sambamba" bin)
+ #t))))))
+ (native-inputs
+ `(("ldc" ,ldc)
+ ("rdmd" ,rdmd)
+ ("biod"
+ ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biod/BioD.git";)
+ (commit commit)))
+ (file-name (string-append "biod-"
+ (string-take commit 9)
+ "-checkout"))
+ (sha256
+ (base32
+ "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
+ (inputs
+ `(("lz4" ,lz4)
+ ("htslib" ,htslib-for-sambamba)))
+ (home-page "http://lomereiter.github.io/sambamba";)
+ (synopsis "Tools for working with SAM/BAM data")
+ (description "Sambamba is a high performance modern robust and
+fast tool (and library), written in the D programming language, for
+working with SAM and BAM files. Current parallelised functionality is
+an important subset of samtools functionality, including view, index,
+sort, markdup, and depth.")
+ (license license:gpl2+)))
--
2.11.1
--- End Message ---
--- Begin Message ---
|
Subject: |
Re: bug#25996: Sambamba |
|
Date: |
Fri, 10 Mar 2017 10:17:20 +0100 |
|
User-agent: |
mu4e 0.9.18; emacs 25.1.1 |
Pjotr Prins <address@hidden> writes:
> Sambamba just got a new release 0.6.6. I have a package here
>
>
> https://github.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/sambamba.scm
>
> which deals with undeaD and actually enforces dependencies of
> externally called samtools and bcftools. 0.6.6 fixes a nasty bug, but
> requires a patched version of the ldc compiler (not in GNU Guix):
>
>
> https://github.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/ldc.scm#L119
>
> https://github.com/genenetwork/guix-bioinformatics/blob/master/ldc-druntime-finiTLSRanges.patch
Oh, I see. I tried to update my package after seeing your message, but
requiring a patched version of the compiler makes this more challenging.
> I suggest we add 0.6.5 to Guix now and update to the newer version when
> the dust settles.
I pushed 0.6.5 to master with commit 5ded35d89. Thanks for taking a
look!
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
https://elephly.net
--- End Message ---