From: <ricardo.wurmus@mdc-berlin.de>
To: 29394@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: [bug#29394] [PATCH 05/12] gnu: java-htsjdk: Update to 2.3.0.
Date: Wed, 22 Nov 2017 12:30:35 +0100 [thread overview]
Message-ID: <20171122113042.1734-5-ricardo.wurmus@mdc-berlin.de> (raw)
In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de>
From: Ricardo Wurmus <rekado@elephly.net>
* 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 a8d7361ff..6c71d7362 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
--
2.14.1
next prev parent reply other threads:[~2017-11-22 11:33 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-11-22 11:21 [bug#29394] [PATCH 00/12] Add Java dependencies for FastQC Ricardo Wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 01/12] gnu: Add java-snappy-1 ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 02/12] gnu: Add javacc ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 03/12] gnu: Add javacc-4 ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 04/12] gnu: Add java-commons-jexl-2 ricardo.wurmus
2017-11-22 11:30 ` ricardo.wurmus [this message]
2017-11-22 11:30 ` [bug#29394] [PATCH 06/12] gnu: Add java-picard ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 07/12] gnu: Add java-cofoja ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 08/12] gnu: Add java-commons-bcel ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 09/12] gnu: Add ant-apache-bcel ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 10/12] gnu: Add ant-junit ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 11/12] gnu: Add java-picard-1.113 ricardo.wurmus
2017-11-22 11:30 ` [bug#29394] [PATCH 12/12] gnu: Add java-jbzip2 ricardo.wurmus
2017-11-27 20:56 ` bug#29394: " Ricardo Wurmus
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20171122113042.1734-5-ricardo.wurmus@mdc-berlin.de \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=29394@debbugs.gnu.org \
--cc=rekado@elephly.net \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).