me
/
guix
Archived
1
0
Fork 0
Code

gnu: stringtie: Update to 2.2.0. 

* gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0.
[source]: Simplify snippet.
[arguments]: Add make-flags; update build phases.
[inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and
libdeflate.
[license]: Change to Expat license.
Ricardo Wurmus 2022-01-11 14:18:06 +01:00
parent 9966f98b1b
commit 946fd9be16
No known key found for this signature in database
GPG Key ID: 197A5888235FACAC
1 changed files with 15 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
gnu/packages/bioinformatics.scm
View File

@ -7380,22 +7380,25 @@ against local background noises.")
(define-public stringtie (define-public stringtie
(package (package
(name "stringtie") (name "stringtie")
(version "1.2.1") (version "2.2.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
"stringtie-" version ".tar.gz")) "stringtie-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) "08w3ish4y9kf9acp7k38iwi8ixa6j51m6qyf0vvfj7yz78a3ai3x"))
;; This package bundles an annoying amount of third party source
;; code.
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(delete-file-recursively "htslib"))))
(delete-file-recursively "samtools-0.1.18")
#t))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ;no test suite `(#:tests? #f ;no test suite
#:make-flags '("LIBDEFLATE=-ldeflate"
"LIBBZ2=-lbz2"
"LIBLZMA=-llzma")
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
;; no configure script ;; no configure script
@ -7403,27 +7406,14 @@ against local background noises.")
(add-before 'build 'use-system-samtools (add-before 'build 'use-system-samtools
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
(("stringtie: \\$\\{BAM\\}/libbam\\.a") ((" -lm") " -lm -lhts")
"stringtie: ")) ((" \\$\\{HTSLIB\\}/libhts\\.a") " "))))
(substitute* '("gclib/GBam.h"
"gclib/GBam.cpp")
(("#include \"(bam|sam|kstring).h\"" _ header)
(string-append "#include <samtools/" header ".h>")))
#t))
(add-after 'unpack 'remove-duplicate-typedef
(lambda _
;; This typedef conflicts with the typedef in
;; glibc-2.25/include/bits/types.h
(substitute* "gclib/GThreads.h"
(("typedef long long __intmax_t;") ""))
#t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(install-file "stringtie" bin) (install-file "stringtie" bin)))))))
#t))))))
(inputs (inputs
(list samtools-0.1 zlib)) (list bzip2 htslib-for-stringtie libdeflate zlib))
(home-page "http://ccb.jhu.edu/software/stringtie/") (home-page "http://ccb.jhu.edu/software/stringtie/")
(synopsis "Transcript assembly and quantification for RNA-Seq data") (synopsis "Transcript assembly and quantification for RNA-Seq data")
(description (description
@ -7436,7 +7426,7 @@ other transcript assemblers, but also alignments of longer sequences that have
been assembled from those reads. To identify differentially expressed genes been assembled from those reads. To identify differentially expressed genes
between experiments, StringTie's output can be processed either by the between experiments, StringTie's output can be processed either by the
Cuffdiff or Ballgown programs.") Cuffdiff or Ballgown programs.")
(license license:artistic2.0))) (license license:expat)))
(define-public taxtastic (define-public taxtastic
(package (package