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-rw-r--r--gnu/packages/bioinformatics.scm43
1 files changed, 18 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4ae1ad0470..35cec1edfb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2590,46 +2590,39 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
(define-public preseq
(package
(name "preseq")
- (version "1.0.2")
+ (version "2.0")
(source (origin
(method url-fetch)
- (uri
- (string-append "http://smithlabresearch.org/downloads/preseq-"
- version ".tar.bz2"))
+ (uri (string-append "https://github.com/smithlabcode/"
+ "preseq/archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
- (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
- (search-patch "preseq-1.0.2-link-with-libbam.patch")))
+ (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
(modules '((guix build utils)))
(snippet
;; Remove bundled samtools.
- '(delete-file-recursively "preseq-master/samtools"))))
+ '(delete-file-recursively "samtools"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
- (add-after
- 'unpack 'enter-dir
- (lambda _
- (chdir "preseq-master")
- #t))
- (add-after
- 'enter-dir 'use-samtools-headers
- (lambda _
- (substitute* '("smithlab_cpp/SAM.cpp"
- "smithlab_cpp/SAM.hpp")
- (("sam.h") "samtools/sam.h"))
- #t))
(delete 'configure))
- #:make-flags (list (string-append "PREFIX="
- (assoc-ref %outputs "out"))
- (string-append "LIBBAM="
- (assoc-ref %build-inputs "samtools")
- "/lib/libbam.a"))))
+ #:make-flags
+ (list (string-append "PREFIX="
+ (assoc-ref %outputs "out"))
+ (string-append "LIBBAM="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/libbam.a")
+ (string-append "SMITHLAB_CPP="
+ (assoc-ref %build-inputs "smithlab-cpp")
+ "/lib")
+ "PROGS=preseq"
+ "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
(inputs
`(("gsl" ,gsl)
("samtools" ,samtools-0.1)
+ ("smithlab-cpp" ,smithlab-cpp)
("zlib" ,zlib)))
(home-page "http://smithlabresearch.org/software/preseq/")
(synopsis "Program for analyzing library complexity")