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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-12-04 15:27:39 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-12-04 15:27:39 +0100 |
| commit | a4e7475edcb58d11e2ebb545a63f4b32ad7bfbd9 (patch) | |
| tree | 2ab2ce9e218dca31911cc2156ac772f699841162 /gnu/packages/bioinformatics.scm | |
| parent | c45c909026965d95fbe404c5a0937f56749b3ddd (diff) | |
| download | guix-a4e7475edcb58d11e2ebb545a63f4b32ad7bfbd9.tar.gz | |
gnu: rsem: Update to 1.3.3.
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3. [arguments]: Build with gnu++11 standard; patch sources for compatibility.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 18 |
1 files changed, 14 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ee03d448f3..bf8aff8fce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6117,7 +6117,7 @@ phylogenies.") (define-public rsem (package (name "rsem") - (version "1.3.1") + (version "1.3.3") (source (origin (method git-fetch) @@ -6125,7 +6125,7 @@ phylogenies.") (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 @@ phylogenies.") #: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"))) |