* [PATCH] gnu: Add bits.
@ 2016-06-29 14:36 Ricardo Wurmus
2016-06-29 16:13 ` Leo Famulari
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2016-06-29 14:36 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (bits): New variable.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a8144a9..11784ab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5186,6 +5186,52 @@ two-dimensional genome scans.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public bits
+ (let ((revision "1")
+ (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
+ (package
+ (name "bits")
+ ;; The version is 2.13.0 even though no release archives have been
+ ;; published as yet.
+ (version (string-append "2.13.0-" revision "." (string-take commit 9)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/arq5x/bits.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no tests included
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'remove-cuda
+ (lambda _
+ (substitute* "Makefile"
+ ((".*_cuda") "")
+ (("(bits_test_intersections) \\\\" _ match) match))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (copy-recursively
+ "bin" (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (inputs
+ `(("gsl" ,gsl)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/arq5x/bits")
+ (synopsis "Implementation of binary interval search algorithm")
+ (description "This package provides an implementation of the
+BITS (Binary Interval Search) algorithm, an approach to interval set
+intersection. It is especially suited for the comparison of diverse genomic
+datasets and the exploration of large datasets of genome
+intervals (e.g. genes, sequence alignments).")
+ (license license:gpl2))))
+
(define-public piranha
;; There is no release tarball for the latest version. The latest commit is
;; older than one year at the time of this writing.
--
2.8.4
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add bits.
2016-06-29 14:36 [PATCH] gnu: Add bits Ricardo Wurmus
@ 2016-06-29 16:13 ` Leo Famulari
2016-06-29 19:15 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Leo Famulari @ 2016-06-29 16:13 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
On Wed, Jun 29, 2016 at 04:36:17PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (bits): New variable.
> + (arguments
> + `(#:tests? #f ;no tests included
How about the tests described in the README?
https://github.com/arq5x/bits
"Now, you can test both the sequential and CUDA versions of the tools by
running the bits_tests scripts. Also, this shell script demonstrates how
to run each of the BITS tools"
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add bits.
2016-06-29 16:13 ` Leo Famulari
@ 2016-06-29 19:15 ` Ricardo Wurmus
2016-07-05 13:05 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2016-06-29 19:15 UTC (permalink / raw)
To: Leo Famulari; +Cc: guix-devel
Leo Famulari <leo@famulari.name> writes:
> On Wed, Jun 29, 2016 at 04:36:17PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (bits): New variable.
>
>> + (arguments
>> + `(#:tests? #f ;no tests included
>
> How about the tests described in the README?
>
> https://github.com/arq5x/bits
>
> "Now, you can test both the sequential and CUDA versions of the tools by
> running the bits_tests scripts. Also, this shell script demonstrates how
> to run each of the BITS tools"
Good idea, I’ll do that.
~~ Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add bits.
2016-06-29 19:15 ` Ricardo Wurmus
@ 2016-07-05 13:05 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2016-07-05 13:05 UTC (permalink / raw)
To: Leo Famulari; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> Leo Famulari <leo@famulari.name> writes:
>
>> On Wed, Jun 29, 2016 at 04:36:17PM +0200, Ricardo Wurmus wrote:
>>> * gnu/packages/bioinformatics.scm (bits): New variable.
>>
>>> + (arguments
>>> + `(#:tests? #f ;no tests included
>>
>> How about the tests described in the README?
>>
>> https://github.com/arq5x/bits
>>
>> "Now, you can test both the sequential and CUDA versions of the tools by
>> running the bits_tests scripts. Also, this shell script demonstrates how
>> to run each of the BITS tools"
>
> Good idea, I’ll do that.
On second thought: I’d rather not. The script doesn’t perform any
tests, it doesn’t compare the output to expected values, so I think it
doesn’t really make sense to run it during the check phase.
I’ll push this as is. Thanks for checking!
~~ Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2016-07-05 13:06 UTC | newest]
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2016-06-29 14:36 [PATCH] gnu: Add bits Ricardo Wurmus
2016-06-29 16:13 ` Leo Famulari
2016-06-29 19:15 ` Ricardo Wurmus
2016-07-05 13:05 ` Ricardo Wurmus
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