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10/17: gnu: Add java-biojava-alignment.
From: |
Ricardo Wurmus |
Subject: |
10/17: gnu: Add java-biojava-alignment. |
Date: |
Sat, 3 Mar 2018 15:28:37 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 22c09c335beff3caa2b434165f09d88267269794
Author: Ricardo Wurmus <address@hidden>
Date: Thu Mar 1 19:41:42 2018 +0100
gnu: Add java-biojava-alignment.
* gnu/packages/bioinformatics.scm (java-biojava-alignment): 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 fbb3264..08d9be4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12212,3 +12212,47 @@ This package provides the core libraries.")
(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
+ (package (inherit java-biojava-core)
+ (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)
+ ("java-biojava-phylo" ,java-biojava-phylo)
+ ("java-forester" ,java-forester)))
+ (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
+
address@hidden
address@hidden implementations of dynamic programming algorithms for sequence
+ alignment;
address@hidden reading and writing of popular alignment file formats;
address@hidden a single-, or multi- threaded multiple sequence alignment
algorithm.
address@hidden itemize\n")))
- 03/17: gnu: Add java-jtransforms., (continued)
- 03/17: gnu: Add java-jtransforms., Ricardo Wurmus, 2018/03/03
- 05/17: gnu: Add java-biojava-core., Ricardo Wurmus, 2018/03/03
- 06/17: gnu: Add java-openchart2., Ricardo Wurmus, 2018/03/03
- 04/17: gnu: Add java-jdistlib., Ricardo Wurmus, 2018/03/03
- 09/17: gnu: Add java-biojava-phylo., Ricardo Wurmus, 2018/03/03
- 08/17: gnu: Add java-forester-1.005., Ricardo Wurmus, 2018/03/03
- 01/17: gnu: Add java-la4j., Ricardo Wurmus, 2018/03/03
- 14/17: gnu: Add java-htsjdk-latest., Ricardo Wurmus, 2018/03/03
- 07/17: gnu: Add java-forester., Ricardo Wurmus, 2018/03/03
- 11/17: gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/03
- 10/17: gnu: Add java-biojava-alignment.,
Ricardo Wurmus <=
- 12/17: gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/03
- 13/17: gnu: Add java-biojava-alignment-4.0., Ricardo Wurmus, 2018/03/03
- 16/17: gnu: Add java-picard-2.10.3., Ricardo Wurmus, 2018/03/03
- 15/17: gnu: Add java-htsjdk-2.10.1., Ricardo Wurmus, 2018/03/03
- 17/17: gnu: Add dropseq-tools., Ricardo Wurmus, 2018/03/03