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-rw-r--r--gnu/packages/bioinformatics.scm81
1 files changed, 75 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b76aadc6a2..c49b0a9e17 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -922,6 +922,75 @@ also includes an interface for tabix.")
(define-public python2-pysam
(package-with-python2 python-pysam))
+(define-public python-twobitreader
+ (package
+ (name "python-twobitreader")
+ (version "3.1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "twobitreader" version))
+ (sha256
+ (base32
+ "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
+ (properties `((python2-variant . ,(delay python2-twobitreader))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-sphinx" ,python-sphinx)))
+ (home-page "https://github.com/benjschiller/twobitreader")
+ (synopsis "Python library for reading .2bit files")
+ (description
+ "twobitreader is a Python library for reading .2bit files as used by the
+UCSC genome browser.")
+ (license license:artistic2.0)))
+
+(define-public python2-twobitreader
+ (let ((base (package-with-python2 (strip-python2-variant python-twobitreader))))
+ (package
+ (inherit base)
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs base))))))
+
+(define-public python-plastid
+ (package
+ (name "python-plastid")
+ (version "0.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "plastid" version))
+ (sha256
+ (base32
+ "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
+ (properties `((python2-variant . ,(delay python2-plastid))))
+ (build-system python-build-system)
+ (arguments
+ ;; Some test files are not included.
+ `(#:tests? #f))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)
+ ("python-pandas" ,python-pandas)
+ ("python-pysam" ,python-pysam)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-biopython" ,python-biopython)
+ ("python-twobitreader" ,python-twobitreader)))
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-nose" ,python-nose)))
+ (home-page "https://github.com/joshuagryphon/plastid")
+ (synopsis "Python library for genomic analysis")
+ (description
+ "plastid is a Python library for genomic analysis – in particular,
+high-throughput sequencing data – with an emphasis on simplicity.")
+ (license license:bsd-3)))
+
+(define-public python2-plastid
+ (let ((base (package-with-python2 (strip-python2-variant python-plastid))))
+ (package
+ (inherit base)
+ ;; setuptools is required at runtime
+ (propagated-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-propagated-inputs base))))))
+
(define-public cd-hit
(package
(name "cd-hit")
@@ -2075,9 +2144,9 @@ HMMs).")
from high-throughput sequencing assays.")
(license license:gpl3+)))
-(define-public htsjdk
+(define-public java-htsjdk
(package
- (name "htsjdk")
+ (name "java-htsjdk")
(version "1.129")
(source (origin
(method url-fetch)
@@ -3012,9 +3081,9 @@ any particular back-end implementation, and supports use of multiple back-ends
simultaneously.")
(license license:public-domain)))
-(define-public ngs-java
+(define-public java-ngs
(package (inherit ngs-sdk)
- (name "ngs-java")
+ (name "java-ngs")
(arguments
`(,@(substitute-keyword-arguments
`(#:modules ((guix build gnu-build-system)
@@ -3077,7 +3146,7 @@ simultaneously.")
(string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk"))
(string-append "--with-ngs-java-prefix="
- (assoc-ref inputs "ngs-java"))
+ (assoc-ref inputs "java-ngs"))
(string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5"))))))
(alist-cons-after
@@ -3103,7 +3172,7 @@ simultaneously.")
(inputs
`(("libxml2" ,libxml2)
("ngs-sdk" ,ngs-sdk)
- ("ngs-java" ,ngs-java)
+ ("java-ngs" ,java-ngs)
("libmagic" ,file)
("hdf5" ,hdf5)))
(native-inputs `(("perl" ,perl)))