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gnu: java-htsjdk: Update to 2.3.0. 

* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0.
[arguments]: Build with JDK 8.
[inputs]: Add java-ngs, java-snappy, java-commons-compress,
java-commons-logging-minimal, java-commons-jexl-2, and java-xz.
[native-inputs]: Add java-testng.
This commit is contained in:
Ricardo Wurmus 2017-11-18 23:58:59 +01:00
parent 9e325e8c05
commit bd94b6f850
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GPG Key ID: 197A5888235FACAC
1 changed files with 18 additions and 6 deletions
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@ -2961,7 +2961,7 @@ from high-throughput sequencing assays.")
(define-public java-htsjdk (define-public java-htsjdk
(package (package
(name "java-htsjdk") (name "java-htsjdk")
(version "1.129") (version "2.3.0") ; last version without build dependency on gradle
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -2970,15 +2970,18 @@ from high-throughput sequencing assays.")
(file-name (string-append name "-" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
(modules '((guix build utils))) (modules '((guix build utils)))
;; remove build dependency on git (snippet
(snippet '(substitute* "build.xml" ;; Delete pre-built binaries
(("failifexecutionfails=\"true\"") '(begin
"failifexecutionfails=\"false\""))))) (delete-file-recursively "lib")
(mkdir-p "lib")
#t))))
(build-system ant-build-system) (build-system ant-build-system)
(arguments (arguments
`(#:tests? #f ; test require Internet access `(#:tests? #f ; test require Internet access
#:jdk ,icedtea-8
#:make-flags #:make-flags
(list (string-append "-Ddist=" (assoc-ref %outputs "out") (list (string-append "-Ddist=" (assoc-ref %outputs "out")
"/share/java/htsjdk/")) "/share/java/htsjdk/"))
@ -2987,6 +2990,15 @@ from high-throughput sequencing assays.")
(modify-phases %standard-phases (modify-phases %standard-phases
;; The build phase also installs the jars ;; The build phase also installs the jars
(delete 'install)))) (delete 'install))))
(inputs
`(("java-ngs" ,java-ngs)
("java-snappy-1" ,java-snappy-1)
("java-commons-compress" ,java-commons-compress)
("java-commons-logging-minimal" ,java-commons-logging-minimal)
("java-commons-jexl-2" ,java-commons-jexl-2)
("java-xz" ,java-xz)))
(native-inputs
`(("java-testng" ,java-testng)))
(home-page "http://samtools.github.io/htsjdk/") (home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats") (synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description (description