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01/03: gnu: Add pbbam.
From: |
guix-commits |
Subject: |
01/03: gnu: Add pbbam. |
Date: |
Mon, 18 Mar 2019 09:48:01 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 55154c5f40d0b2782f98f5e2431f3c845ed798cd
Author: Ricardo Wurmus <address@hidden>
Date: Wed Mar 13 18:14:24 2019 +0100
gnu: Add pbbam.
* gnu/packages/bioinformatics.scm (pbbam): New variable.
---
gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3364a35..43835cf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -40,6 +40,7 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system haskell)
+ #:use-module (guix build-system meson)
#:use-module (guix build-system ocaml)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
@@ -477,6 +478,62 @@ BED, GFF/GTF, VCF.")
(base32
"0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5"))))))
+(define-public pbbam
+ (package
+ (name "pbbam")
+ (version "0.23.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/PacificBiosciences/pbbam.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0h9gkrpf2lrxklxp72xfl5bi3h5zcm5hprrya9gf0hr3xwlbpp0x"))))
+ (build-system meson-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'find-googletest
+ (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@@address@hidden/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")))
+ ;; These libraries are listed as "Required" in the pkg-config file.
+ (propagated-inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (inputs
+ `(("boost" ,boost)
+ ("samtools" ,samtools)))
+ (native-inputs
+ `(("googletest" ,googletest)
+ ("pkg-config" ,pkg-config)
+ ("python" ,python-wrapper))) ; for tests
+ (home-page "https://github.com/PacificBiosciences/pbbam")
+ (synopsis "Work with PacBio BAM files")
+ (description
+ "The pbbam software package provides components to create, query, and
+edit PacBio BAM files and associated indices. These components include a core
+C++ library, bindings for additional languages, and command-line utilities.
+This library is not intended to be used as a general-purpose BAM utility - all
+input and output BAMs must adhere to the PacBio BAM format specification.
+Non-PacBio BAMs will cause exceptions to be thrown.")
+ (license license:bsd-3)))
+
(define-public ribotaper
(package
(name "ribotaper")