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05/12: gnu: java-htsjdk: Update to 2.3.0.
From: |
Ricardo Wurmus |
Subject: |
05/12: gnu: java-htsjdk: Update to 2.3.0. |
Date: |
Mon, 27 Nov 2017 06:13:14 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit bd94b6f850b2be6953a2d8688b2be78cac8d341a
Author: Ricardo Wurmus <address@hidden>
Date: Sat Nov 18 23:58:59 2017 +0100
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.
---
gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++------
1 file changed, 18 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2a2d7f8..5164da0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2961,7 +2961,7 @@ from high-throughput sequencing assays.")
(define-public java-htsjdk
(package
(name "java-htsjdk")
- (version "1.129")
+ (version "2.3.0") ; last version without build dependency on gradle
(source (origin
(method url-fetch)
(uri (string-append
@@ -2970,15 +2970,18 @@ from high-throughput sequencing assays.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
+ "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
(modules '((guix build utils)))
- ;; remove build dependency on git
- (snippet '(substitute* "build.xml"
- (("failifexecutionfails=\"true\"")
- "failifexecutionfails=\"false\"")))))
+ (snippet
+ ;; Delete pre-built binaries
+ '(begin
+ (delete-file-recursively "lib")
+ (mkdir-p "lib")
+ #t))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; test require Internet access
+ #:jdk ,icedtea-8
#:make-flags
(list (string-append "-Ddist=" (assoc-ref %outputs "out")
"/share/java/htsjdk/"))
@@ -2987,6 +2990,15 @@ from high-throughput sequencing assays.")
(modify-phases %standard-phases
;; The build phase also installs the jars
(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/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
- branch master updated (9cc51d1 -> 776d2fb), Ricardo Wurmus, 2017/11/27
- 02/12: gnu: Add javacc., Ricardo Wurmus, 2017/11/27
- 05/12: gnu: java-htsjdk: Update to 2.3.0.,
Ricardo Wurmus <=
- 10/12: gnu: Add ant-junit., Ricardo Wurmus, 2017/11/27
- 08/12: gnu: Add java-commons-bcel., Ricardo Wurmus, 2017/11/27
- 04/12: gnu: Add java-commons-jexl-2., Ricardo Wurmus, 2017/11/27
- 07/12: gnu: Add java-cofoja., Ricardo Wurmus, 2017/11/27
- 09/12: gnu: Add ant-apache-bcel., Ricardo Wurmus, 2017/11/27
- 01/12: gnu: Add java-snappy-1., Ricardo Wurmus, 2017/11/27
- 03/12: gnu: Add javacc-4., Ricardo Wurmus, 2017/11/27
- 12/12: gnu: Add java-jbzip2., Ricardo Wurmus, 2017/11/27
- 06/12: gnu: Add java-picard., Ricardo Wurmus, 2017/11/27
- 11/12: gnu: Add java-picard-1.113., Ricardo Wurmus, 2017/11/27