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gnu: flexbar: Update to 3.4.0. 

* gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0.
[source]: Fetch from git.
[arguments]: Adjust check and install phases.
[home-page]: Update to new home at Github.
[license]: Change to bsd-3.
This commit is contained in:
Ricardo Wurmus 2018-10-21 23:05:11 +02:00
parent 4d93a9a36c
commit f8ee22fc8b
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1 changed files with 20 additions and 19 deletions
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@ -2607,38 +2607,39 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(define-public flexbar (define-public flexbar
(package (package
(name "flexbar") (name "flexbar")
(version "2.5") (version "3.4.0")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (uri (git-reference
(string-append "mirror://sourceforge/flexbar/" (url "https://github.com/seqan/flexbar.git")
version "/flexbar_v" version "_src.tgz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments (arguments
`(#:configure-flags (list `(#:phases
(string-append "-DFLEXBAR_BINARY_DIR="
(assoc-ref %outputs "out")
"/bin/"))
#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'check (replace 'check
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(setenv "PATH" (string-append (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
(assoc-ref outputs "out") "/bin:" (with-directory-excursion "../source/test"
(getenv "PATH"))) (invoke "bash" "flexbar_test.sh"))
(chdir "../flexbar_v2.5_src/test") #t))
(zero? (system* "bash" "flexbar_validate.sh")))) (replace 'install
(delete 'install)))) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/")))
(install-file "flexbar" bin))
#t)))))
(inputs (inputs
`(("tbb" ,tbb) `(("tbb" ,tbb)
("zlib" ,zlib))) ("zlib" ,zlib)))
(native-inputs (native-inputs
`(("pkg-config" ,pkg-config) `(("pkg-config" ,pkg-config)
("seqan" ,seqan))) ("seqan" ,seqan)))
(home-page "http://flexbar.sourceforge.net") (home-page "https://github.com/seqan/flexbar")
(synopsis "Barcode and adapter removal tool for sequencing platforms") (synopsis "Barcode and adapter removal tool for sequencing platforms")
(description (description
"Flexbar preprocesses high-throughput nucleotide sequencing data "Flexbar preprocesses high-throughput nucleotide sequencing data
@ -2647,7 +2648,7 @@ Moreover, trimming and filtering features are provided. Flexbar increases
read mapping rates and improves genome and transcriptome assemblies. It read mapping rates and improves genome and transcriptome assemblies. It
supports next-generation sequencing data in fasta/q and csfasta/q format from supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.") Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3))) (license license:bsd-3)))
(define-public fraggenescan (define-public fraggenescan
(package (package