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-rw-r--r--gnu/packages/bioinformatics.scm66
1 files changed, 49 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b3d882761b..4dd2ee6f92 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -26,6 +26,7 @@
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
+ #:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system perl)
@@ -2002,24 +2003,17 @@ from high-throughput sequencing assays.")
(snippet '(substitute* "build.xml"
(("failifexecutionfails=\"true\"")
"failifexecutionfails=\"false\"")))))
- (build-system gnu-build-system)
+ (build-system ant-build-system)
(arguments
- `(#:modules ((srfi srfi-1)
- (guix build gnu-build-system)
- (guix build utils))
- #:phases (alist-replace
- 'build
- (lambda _
- (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
- (zero? (system* "ant" "all"
- (string-append "-Ddist="
- (assoc-ref %outputs "out")
- "/share/java/htsjdk/"))))
- (fold alist-delete %standard-phases
- '(configure install check)))))
- (native-inputs
- `(("ant" ,ant)
- ("jdk" ,icedtea "jdk")))
+ `(#:tests? #f ; test require Internet access
+ #:make-flags
+ (list (string-append "-Ddist=" (assoc-ref %outputs "out")
+ "/share/java/htsjdk/"))
+ #:build-target "all"
+ #:phases
+ (modify-phases %standard-phases
+ ;; The build phase also installs the jars
+ (delete 'install))))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
@@ -2556,6 +2550,44 @@ the phenotype as it models the data.")
generated using the PacBio Iso-Seq protocol.")
(license license:bsd-3))))
+(define-public pyicoteo
+ (package
+ (name "pyicoteo")
+ (version "2.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
+ "pyicoteo/get/v" version ".tar.bz2"))
+ (file-name (string-append name "-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; does not work with Python 3
+ #:tests? #f)) ; there are no tests
+ (inputs
+ `(("python2-matplotlib" ,python2-matplotlib)))
+ (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
+ (synopsis "Analyze high-throughput genetic sequencing data")
+ (description
+ "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
+sequencing data. It works with genomic coordinates. There are currently six
+different command-line tools:
+
+@enumerate
+@item pyicoregion: for generating exploratory regions automatically;
+@item pyicoenrich: for differential enrichment between two conditions;
+@item pyicoclip: for calling CLIP-Seq peaks without a control;
+@item pyicos: for genomic coordinates manipulation;
+@item pyicoller: for peak calling on punctuated ChIP-Seq;
+@item pyicount: to count how many reads from N experiment files overlap in a
+ region file;
+@item pyicotrocol: to combine operations from pyicoteo.
+@end enumerate\n")
+ (license license:gpl3+)))
+
(define-public prodigal
(package
(name "prodigal")