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gnu: pbbam: Update to 1.7.0.

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* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
This commit is contained in:
Ricardo Wurmus 2021-12-07 18:10:07 +01:00
parent b764d10e91
commit fc797a3e8f
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1 changed files with 17 additions and 19 deletions
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36
gnu/packages/bioinformatics.scm
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@ -608,40 +608,38 @@ (define-public pbcopper
(define-public pbbam
(package
(name "pbbam")
(version "0.23.0")
(version "1.7.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/pbbam")
(commit version)))
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0h9gkrpf2lrxklxp72xfl5bi3h5zcm5hprrya9gf0hr3xwlbpp0x"))))
"1avdm5hwhr5ls79017blyalx1npzbf1aa6dgb6j6lg8sq4nk9yyg"))))
(build-system meson-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'find-googletest
(add-after 'unpack 'patch-tests
(lambda* (#:key inputs #:allow-other-keys)
;; It doesn't find gtest_main because there's no pkg-config file
;; for it. Find it another way.
(substitute* "tests/meson.build"
(("pbbam_gtest_dep = dependency\\('gtest_main'.*")
(format #f "cpp = meson.get_compiler('cpp')
pbbam_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
(assoc-ref inputs "googletest"))))
#t)))
;; TODO: tests/pbbam_test cannot be linked
;; ld: tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o:
;; undefined reference to symbol '_ZTIN7testing4TestE'
;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so:
;; error adding symbols: DSO missing from command line
#:tests? #f
#:configure-flags '("-Dtests=false")))
;; Disable this test. I tried fixing it by including
;; optional_io.hpp, but there's a type error.
(substitute* "tests/src/meson.build"
(("'test_ReadGroupInfo.cpp',") ""))
#;
(substitute* "include/pbbam/ReadGroupInfo.h"
(("#include <boost/optional.hpp>" m)
(string-append m "\n#include <boost/optional/optional_io.hpp>")))
(substitute* '("tests/scripts/cram/_test.py"
"tests/scripts/cram/_main.py")
(("'/bin/sh'")
(string-append "'" (which "sh") "'"))))))))
;; These libraries are listed as "Required" in the pkg-config file.
(propagated-inputs
`(("htslib" ,htslib)
("pbcopper" ,pbcopper)
("zlib" ,zlib)))
(inputs
`(("boost" ,boost)