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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.
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1 changed files with 14 additions and 4 deletions
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@ -6117,7 +6117,7 @@ (define-public raxml
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(define-public rsem
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(define-public rsem
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(package
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(package
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(name "rsem")
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(name "rsem")
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(version "1.3.1")
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(version "1.3.3")
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(source
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(source
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(origin
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(origin
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(method git-fetch)
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(method git-fetch)
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@ -6125,7 +6125,7 @@ (define-public rsem
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(url "https://github.com/deweylab/RSEM")
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(url "https://github.com/deweylab/RSEM")
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(commit (string-append "v" version))))
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(commit (string-append "v" version))))
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(sha256
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(sha256
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(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
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(base32 "1yl4i7z20n2p84j1lmk15aiak3yqc6fiw0q5a4pndw7pxfiq3rzp"))
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(file-name (git-file-name name version))
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(file-name (git-file-name name version))
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(modules '((guix build utils)))
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(modules '((guix build utils)))
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(snippet
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(snippet
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@ -6149,12 +6149,22 @@ (define-public rsem
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#:phases
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#:phases
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(modify-phases %standard-phases
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(modify-phases %standard-phases
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;; No "configure" script.
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;; No "configure" script.
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;; Do not build bundled samtools library.
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(replace 'configure
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(replace 'configure
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(lambda _
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(lambda _
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(substitute* "Makefile"
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(substitute* "Makefile"
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(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
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(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
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(("^\\$\\(SAMLIBS\\).*") ""))))
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;; Do not build bundled samtools library.
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(("^\\$\\(SAMLIBS\\).*") "")
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;; Needed for Boost
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(("gnu\\+\\+98") "gnu++11"))
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;; C++11 compatibility
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(substitute* "buildReadIndex.cpp"
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(("success = \\(getline")
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"success = (bool)(getline"))
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(substitute* '("PairedEndHit.h"
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"SingleHit.h")
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(("return \\(in>>sid>>pos")
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"return (bool)(in>>sid>>pos"))))
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(replace 'install
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (string-append (assoc-ref outputs "out")))
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(let* ((out (string-append (assoc-ref outputs "out")))
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