guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 1ffec44bf2646fb724efdf070e8f9b7f5819bc8b
Author: Andreas Enge <[email protected]>
AuthorDate: Mon Nov 24 11:11:10 2025 +0100
gnu: Remove pbbam.
* gnu/packages/bioinformatics.scm (pbbam): Delete variable.
Change-Id: I75ff8816ca4c37508864890ee2561b3947a53dc1
---
gnu/packages/bioinformatics.scm | 51 -----------------------------------------
1 file changed, 51 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5f5dc2c2bc..b37efeb1f7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1962,57 +1962,6 @@ quantification tools so that it can be used with the
Sleuth differential
analysis package.")
(license license:bsd-3))))
-(define-public pbbam
- (package
- (name "pbbam")
- (version "2.1.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/PacificBiosciences/pbbam";)
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1iyazi3l7dswpfxh39k5j7ydi0ywja0579xz3r6l9kkwz2n1z6dc"))))
- (build-system meson-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-tests
- (lambda* (#:key inputs #:allow-other-keys)
- ;; 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
- (list htslib-1.14 pbcopper zlib))
- (inputs
- (list boost samtools))
- (native-inputs
- (list googletest
- pkg-config
- 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 pbgzip
(let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
(package
