| Message ID | 20160629143617.28293-1-ricardo.wurmus@mdc-berlin.de |
|---|---|
| State | New |
| Headers | show |
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"
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
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
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.