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gnu: rsem: Update to 1.3.3.

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* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
This commit is contained in:
Ricardo Wurmus 2021-12-04 15:27:39 +01:00
parent c45c909026
commit a4e7475edc
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GPG key ID: 197A5888235FACAC
1 changed files with 14 additions and 4 deletions
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18
gnu/packages/bioinformatics.scm
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@ -6117,7 +6117,7 @@ (define-public raxml
(define-public rsem
(package
(name "rsem")
(version "1.3.1")
(version "1.3.3")
(source
(origin
(method git-fetch)
@ -6125,7 +6125,7 @@ (define-public rsem
(url "https://github.com/deweylab/RSEM")
(commit (string-append "v" version))))
(sha256
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
(base32 "1yl4i7z20n2p84j1lmk15aiak3yqc6fiw0q5a4pndw7pxfiq3rzp"))
(file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
@ -6149,12 +6149,22 @@ (define-public rsem
#:phases
(modify-phases %standard-phases
;; No "configure" script.
;; Do not build bundled samtools library.
(replace 'configure
(lambda _
(substitute* "Makefile"
(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
(("^\\$\\(SAMLIBS\\).*") ""))))
;; Do not build bundled samtools library.
(("^\\$\\(SAMLIBS\\).*") "")
;; Needed for Boost
(("gnu\\+\\+98") "gnu++11"))
;; C++11 compatibility
(substitute* "buildReadIndex.cpp"
(("success = \\(getline")
"success = (bool)(getline"))
(substitute* '("PairedEndHit.h"
"SingleHit.h")
(("return \\(in>>sid>>pos")
"return (bool)(in>>sid>>pos"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))