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-rw-r--r--gnu/packages/bioinformatics.scm105
1 files changed, 66 insertions, 39 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3db67f5427..82cd1e420d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;;
@@ -99,7 +99,7 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
- #:use-module (srfi srfi-26))
+ #:use-module (ice-9 match))
(define-public r-ape
(package
@@ -956,7 +956,7 @@ package provides command line tools using the Bio++ library.")
(define-public blast+
(package
(name "blast+")
- (version "2.4.0")
+ (version "2.6.0")
(source (origin
(method url-fetch)
(uri (string-append
@@ -964,13 +964,15 @@ package provides command line tools using the Bio++ library.")
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
+ "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
+ (patches (search-patches "blast+-fix-makefile.patch"))
(modules '((guix build utils)))
(snippet
'(begin
- ;; Remove bundled bzip2 and zlib
+ ;; Remove bundled bzip2, zlib and pcre.
(delete-file-recursively "c++/src/util/compress/bzip2")
(delete-file-recursively "c++/src/util/compress/zlib")
+ (delete-file-recursively "c++/src/util/regexp")
(substitute* "c++/src/util/compress/Makefile.in"
(("bzip2 zlib api") "api"))
;; Remove useless msbuild directory
@@ -979,9 +981,8 @@ package provides command line tools using the Bio++ library.")
#t))))
(build-system gnu-build-system)
(arguments
- `(;; There are three(!) tests for this massive library, and all fail with
+ `(;; There are two(!) tests for this massive library, and both fail with
;; "unparsable timing stats".
- ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
#:tests? #f
@@ -1014,6 +1015,7 @@ package provides command line tools using the Bio++ library.")
;; Rewrite hardcoded paths to various tools
(substitute* (append '("src/build-system/configure.ac"
"src/build-system/configure"
+ "src/build-system/helpers/run_with_lock.c"
"scripts/common/impl/if_diff.sh"
"scripts/common/impl/run_with_lock.sh"
"src/build-system/Makefile.configurables.real"
@@ -1062,17 +1064,22 @@ package provides command line tools using the Bio++ library.")
(assoc-ref inputs "bzip2"))
(string-append "--with-z="
(assoc-ref inputs "zlib"))
+ (string-append "--with-pcre="
+ (assoc-ref inputs "pcre"))
;; Each library is built twice by default, once
;; with "-static" in its name, and again
;; without.
"--without-static"
"--with-dll"))))))))
- (outputs '("out" ; 19 MB
- "lib" ; 203 MB
- "include")) ; 32 MB
+ (outputs '("out" ; 21 MB
+ "lib" ; 226 MB
+ "include")) ; 33 MB
(inputs
`(("bzip2" ,bzip2)
- ("zlib" ,zlib)))
+ ("zlib" ,zlib)
+ ("pcre" ,pcre)
+ ("perl" ,perl)
+ ("python" ,python-wrapper)))
(native-inputs
`(("cpio" ,cpio)))
(home-page "http://blast.ncbi.nlm.nih.gov")
@@ -1309,14 +1316,14 @@ splice junctions between exons.")
(define-public bwa
(package
(name "bwa")
- (version "0.7.12")
+ (version "0.7.15")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
version ".tar.bz2"))
(sha256
(base32
- "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
+ "0585ikg0gv0mpyw9iq0bq9n0hr95867bbv8jbzs9pk4slkpsymig"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
@@ -1562,15 +1569,16 @@ high-throughput sequencing data – with an emphasis on simplicity.")
(define-public cd-hit
(package
(name "cd-hit")
- (version "4.6.6")
+ (version "4.6.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/weizhongli/cdhit"
"/releases/download/V" version
- "/cd-hit-v" version "-2016-0711.tar.gz"))
+ "/cd-hit-v" version
+ "-2017-0621-source.tar.gz"))
(sha256
(base32
- "1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p"))))
+ "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
@@ -1590,7 +1598,7 @@ high-throughput sequencing data – with an emphasis on simplicity.")
(("__DATE__") "\"0\"")
(("\", %s, \" __TIME__ \"\\\\n\", date") ""))
#t))
- ;; The "install" target does not create the target directory
+ ;; The "install" target does not create the target directory.
(add-before 'install 'create-target-dir
(lambda* (#:key outputs #:allow-other-keys)
(mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
@@ -2050,11 +2058,29 @@ trees (phylogenies) and characters.")
(native-inputs `(("python2-nose" ,python2-nose)
,@(package-native-inputs base))))))
+(define-public python-py2bit
+ (package
+ (name "python-py2bit")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "py2bit" version))
+ (sha256
+ (base32
+ "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/dpryan79/py2bit")
+ (synopsis "Access 2bit files using lib2bit")
+ (description
+ "This package provides Python bindings for lib2bit to access 2bit files
+with Python.")
+ (license license:expat)))
(define-public deeptools
(package
(name "deeptools")
- (version "2.1.1")
+ (version "2.5.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/fidelram/deepTools/"
@@ -2062,22 +2088,20 @@ trees (phylogenies) and characters.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
+ "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
(build-system python-build-system)
- (arguments
- `(#:python ,python-2))
(inputs
- `(("python-scipy" ,python2-scipy)
- ("python-numpy" ,python2-numpy)
- ("python-numpydoc" ,python2-numpydoc)
- ("python-matplotlib" ,python2-matplotlib)
- ("python-bx-python" ,python2-bx-python)
- ("python-pysam" ,python2-pysam)
- ("python-pybigwig" ,python2-pybigwig)))
+ `(("python-scipy" ,python-scipy)
+ ("python-numpy" ,python-numpy)
+ ("python-numpydoc" ,python-numpydoc)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pysam" ,python-pysam)
+ ("python-py2bit" ,python-py2bit)
+ ("python-pybigwig" ,python-pybigwig)))
(native-inputs
- `(("python-mock" ,python2-mock) ;for tests
- ("python-nose" ,python2-nose) ;for tests
- ("python-pytz" ,python2-pytz))) ;for tests
+ `(("python-mock" ,python-mock) ;for tests
+ ("python-nose" ,python-nose) ;for tests
+ ("python-pytz" ,python-pytz))) ;for tests
(home-page "https://github.com/fidelram/deepTools")
(synopsis "Tools for normalizing and visualizing deep-sequencing data")
(description
@@ -2094,7 +2118,7 @@ identify enrichments with functional annotations of the genome.")
(define-public diamond
(package
(name "diamond")
- (version "0.9.8")
+ (version "0.9.9")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2103,7 +2127,7 @@ identify enrichments with functional annotations of the genome.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "04f501vj3i95i2b4n60831k00ljalifrq33419bbz0y3sjlmcnj3"))))
+ "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
@@ -2711,7 +2735,8 @@ comment or quality sections.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
+ "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
+ (patches (search-patches "gemma-intel-compat.patch"))))
(inputs
`(("gsl" ,gsl)
("lapack" ,lapack)
@@ -2719,11 +2744,13 @@ comment or quality sections.")
(build-system gnu-build-system)
(arguments
`(#:make-flags
- '(,@(if (any (cute string-prefix? <> (or (%current-system)
- (%current-target-system)))
- '("x86_64" "mips64el" "aarch64"))
- '("FORCE_DYNAMIC=1") ; use shared libs
- '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")))
+ '(,@(match (%current-system)
+ ("x86_64-linux"
+ '("FORCE_DYNAMIC=1"))
+ ("i686-linux"
+ '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
+ (_
+ '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
#:phases
(modify-phases %standard-phases
(delete 'configure)
generated by cgit v1.2.3 (git 2.25.4) at 2024-06-30 00:42:32 +0000