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03/09: gnu: pbbam: Update to 1.7.0.
From: |
guix-commits |
Subject: |
03/09: gnu: pbbam: Update to 1.7.0. |
Date: |
Tue, 7 Dec 2021 17:52:13 -0500 (EST) |
rekado pushed a commit to branch core-updates-frozen
in repository guix.
commit fc797a3e8f4e8a77d2a07fb9ef42bd0b962a0acb
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Dec 7 18:10:07 2021 +0100
gnu: pbbam: Update to 1.7.0.
* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
---
gnu/packages/bioinformatics.scm | 36 +++++++++++++++++-------------------
1 file changed, 17 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 50f1a18..c7413bd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -608,40 +608,38 @@ and utilities for PacBio C++ applications.")
(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)
- branch core-updates-frozen updated (8dcf062 -> 5fb1ba8), guix-commits, 2021/12/07
- 01/09: gnu: Add pbcopper., guix-commits, 2021/12/07
- 03/09: gnu: pbbam: Update to 1.7.0.,
guix-commits <=
- 08/09: gnu: blasr: Update to 5.3.5., guix-commits, 2021/12/07
- 02/09: gnu: bwa-pssm: Fix build., guix-commits, 2021/12/07
- 04/09: gnu: clipper: Update to 2.0.1., guix-commits, 2021/12/07
- 05/09: gnu: htseq: Update to 0.12.3., guix-commits, 2021/12/07
- 06/09: gnu: blasr-libcpp: Update to 5.3.5., guix-commits, 2021/12/07
- 07/09: gnu: blasr: Remove trailing #T., guix-commits, 2021/12/07
- 09/09: gnu: newick-utils: Pass -fcommon to compiler., guix-commits, 2021/12/07