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gnu: samtools: Update to 1.3. 

* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
This commit is contained in:
Ricardo Wurmus 2016-01-13 15:09:00 +01:00
parent 93ce8a8e00
commit c44734115a
1 changed files with 12 additions and 27 deletions
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39
gnu/packages/bioinformatics.scm
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@ -2388,7 +2388,7 @@ distribution, coverage uniformity, strand specificity, etc.")
(define-public samtools (define-public samtools
(package (package
(name "samtools") (name "samtools")
(version "1.2") (version "1.3")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -2397,38 +2397,23 @@ distribution, coverage uniformity, strand specificity, etc.")
version "/samtools-" version ".tar.bz2")) version "/samtools-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2")))) "03mnf0mhbfwhqlqfslrhfnw68s3g0fs1as354i9a584mqw1l1smy"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(;; There are 87 test failures when building on non-64-bit architectures `(#:modules ((ice-9 ftw)
;; due to invalid test data. This has since been fixed upstream (see
;; <https://github.com/samtools/samtools/pull/307>), but as there has
;; not been a new release we disable the tests for all non-64-bit
;; systems.
#:tests? ,(string=? (or (%current-system) (%current-target-system))
"x86_64-linux")
#:modules ((ice-9 ftw)
(ice-9 regex) (ice-9 regex)
(guix build gnu-build-system) (guix build gnu-build-system)
(guix build utils)) (guix build utils))
#:make-flags (list "LIBCURSES=-lncurses" #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
(string-append "prefix=" (assoc-ref %outputs "out"))) #:configure-flags (list "--with-ncurses")
#:phases #:phases
(alist-cons-after (alist-cons-after
'unpack 'unpack 'patch-tests
'patch-tests (lambda _
(lambda* (#:key inputs #:allow-other-keys) (substitute* "test/test.pl"
(let ((bash (assoc-ref inputs "bash"))) ;; The test script calls out to /bin/bash
(substitute* "test/test.pl" (("/bin/bash") (which "bash")))
;; The test script calls out to /bin/bash #t)
(("/bin/bash")
(string-append bash "/bin/bash"))
;; There are two failing tests upstream relating to the "stats"
;; subcommand in test_usage_subcommand ("did not have Usage"
;; and "usage did not mention samtools stats"), so we disable
;; them.
(("(test_usage_subcommand\\(.*\\);)" cmd)
(string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
(alist-cons-after (alist-cons-after
'install 'install-library 'install 'install-library
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
@ -2443,7 +2428,7 @@ distribution, coverage uniformity, strand specificity, etc.")
(install-file file include)) (install-file file include))
(scandir "." (lambda (name) (string-match "\\.h$" name)))) (scandir "." (lambda (name) (string-match "\\.h$" name))))
#t)) #t))
(alist-delete 'configure %standard-phases)))))) %standard-phases)))))
(native-inputs `(("pkg-config" ,pkg-config))) (native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses) (inputs `(("ncurses" ,ncurses)
("perl" ,perl) ("perl" ,perl)