ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-11-19 13:17:10 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: rsem: Update to 1.3.3.

Browse source 
* 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
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 14 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

18
gnu/packages/bioinformatics.scm
View file

@ -6117,7 +6117,7 @@ (define-public raxml
(define-public rsem (define-public rsem
(package (package
(name "rsem") (name "rsem")
(version "1.3.1") (version "1.3.3")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -6125,7 +6125,7 @@ (define-public rsem
(url "https://github.com/deweylab/RSEM") (url "https://github.com/deweylab/RSEM")
(commit (string-append "v" version)))) (commit (string-append "v" version))))
(sha256 (sha256
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) (base32 "1yl4i7z20n2p84j1lmk15aiak3yqc6fiw0q5a4pndw7pxfiq3rzp"))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
@ -6149,12 +6149,22 @@ (define-public rsem
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
;; No "configure" script. ;; No "configure" script.
;; Do not build bundled samtools library.
(replace 'configure (replace 'configure
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n") (("^all : \\$\\(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 (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out"))) (let* ((out (string-append (assoc-ref outputs "out")))