From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: 30666@debbugs.gnu.org
Cc: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: [bug#30666] [PATCH 13/17] gnu: Add java-biojava-alignment-4.0.
Date: Thu, 1 Mar 2018 19:41:45 +0100 [thread overview]
Message-ID: <20180301184149.27239-13-ricardo.wurmus@mdc-berlin.de> (raw)
In-Reply-To: <20180301184149.27239-1-ricardo.wurmus@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
---
gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a01f2c6b8..98c0aff3a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12243,3 +12243,47 @@ contains
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))
+
+(define-public java-biojava-alignment-4.0
+ (package (inherit java-biojava-core-4.0)
+ (name "java-biojava-alignment")
+ (build-system ant-build-system)
+ (arguments
+ `(#:jdk ,icedtea-8
+ #:jar-name "biojava-alignment.jar"
+ #:source-dir "biojava-alignment/src/main/java/"
+ #:test-dir "biojava-alignment/src/test"
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'copy-resources
+ (lambda _
+ (copy-recursively "biojava-alignment/src/main/resources"
+ "build/classes")
+ #t))
+ (add-before 'check 'copy-test-resources
+ (lambda _
+ (copy-recursively "biojava-alignment/src/test/resources"
+ "build/test-classes")
+ #t)))))
+ (propagated-inputs
+ `(("java-log4j-api" ,java-log4j-api)
+ ("java-log4j-core" ,java-log4j-core)
+ ("java-slf4j-api" ,java-slf4j-api)
+ ("java-slf4j-simple" ,java-slf4j-simple)
+ ("java-biojava-core" ,java-biojava-core-4.0)
+ ("java-biojava-phylo" ,java-biojava-phylo-4.0)
+ ("java-forester" ,java-forester-1.005)))
+ (native-inputs
+ `(("java-junit" ,java-junit)
+ ("java-hamcrest-core" ,java-hamcrest-core)))
+ (home-page "http://biojava.org")
+ (synopsis "Biojava API for genetic sequence alignment")
+ (description "The alignment module of BioJava provides an API that
+contains
+
+@itemize
+@item implementations of dynamic programming algorithms for sequence
+ alignment;
+@item reading and writing of popular alignment file formats;
+@item a single-, or multi- threaded multiple sequence alignment algorithm.
+@end itemize\n")))
--
2.15.1
next prev parent reply other threads:[~2018-03-01 18:56 UTC|newest]
Thread overview: 19+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-03-01 17:44 [bug#30666] [PATCH 00/17] Add dropseq-tools Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 01/17] gnu: Add java-la4j Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 02/17] gnu: Add java-jlargearrays Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 03/17] gnu: Add java-jtransforms Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 04/17] gnu: Add java-jdistlib Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 05/17] gnu: Add java-biojava-core Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 06/17] gnu: Add java-openchart2 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 07/17] gnu: Add java-forester Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 08/17] gnu: Add java-forester-1.005 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 09/17] gnu: Add java-biojava-phylo Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 10/17] gnu: Add java-biojava-alignment Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 11/17] gnu: Add java-biojava-core-4.0 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 12/17] gnu: Add java-biojava-phylo-4.0 Ricardo Wurmus
2018-03-01 18:41 ` Ricardo Wurmus [this message]
2018-03-01 18:41 ` [bug#30666] [PATCH 14/17] gnu: Add java-htsjdk-latest Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 15/17] gnu: Add java-htsjdk-2.10.1 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 16/17] gnu: Add java-picard-2.10.3 Ricardo Wurmus
2018-03-01 18:41 ` [bug#30666] [PATCH 17/17] gnu: Add dropseq-tools Ricardo Wurmus
[not found] ` <handler.30666.B.151992663330127.ack@debbugs.gnu.org>
2018-03-03 20:29 ` bug#30666: [PATCH 00/17] " 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
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20180301184149.27239-13-ricardo.wurmus@mdc-berlin.de \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=30666@debbugs.gnu.org \
/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 external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.