diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 91 |
1 files changed, 52 insertions, 39 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67f24a6170..10330cd8b2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4800,66 +4800,79 @@ phylogenies.") (define-public rsem (package (name "rsem") - (version "1.2.20") + (version "1.3.1") (source (origin - (method url-fetch) - (uri - (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deweylab/RSEM.git") + (commit (string-append "v" version)))) (sha256 - (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) - (patches (search-patches "rsem-makefile.patch")) + (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) + (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet '(begin - ;; remove bundled copy of boost + ;; remove bundled copy of boost and samtools (delete-file-recursively "boost") + (delete-file-recursively "samtools-1.3") #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target + #:make-flags + (list (string-append "BOOST=" + (assoc-ref %build-inputs "boost") + "/include/") + (string-append "SAMHEADERS=" + (assoc-ref %build-inputs "htslib") + "/include/htslib/sam.h") + (string-append "SAMLIBS=" + (assoc-ref %build-inputs "htslib") + "/lib/libhts.a")) #:phases (modify-phases %standard-phases ;; No "configure" script. ;; Do not build bundled samtools library. (replace 'configure - (lambda _ - (substitute* "Makefile" - (("^all : sam/libbam.a") "all : ")) - #t)) + (lambda _ + (substitute* "Makefile" + (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n") + (("^\\$\\(SAMLIBS\\).*") "")) + #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (perl (string-append out "/lib/perl5/site_perl"))) - (mkdir-p bin) - (mkdir-p perl) - (for-each (lambda (file) - (install-file file bin)) - (find-files "." "rsem-.*")) - (install-file "rsem_perl_utils.pm" perl)) - #t)) - (add-after - 'install 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (prog) - (wrap-program (string-append out "/bin/" prog) - `("PERL5LIB" ":" prefix - (,(string-append out "/lib/perl5/site_perl"))))) - '("rsem-plot-transcript-wiggles" - "rsem-calculate-expression" - "rsem-generate-ngvector" - "rsem-run-ebseq" - "rsem-prepare-reference"))) - #t))))) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/")) + (perl (string-append out "/lib/perl5/site_perl"))) + (mkdir-p bin) + (mkdir-p perl) + (for-each (lambda (file) + (install-file file bin)) + (find-files "." "rsem-.*")) + (install-file "rsem_perl_utils.pm" perl)) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (prog) + (wrap-program (string-append out "/bin/" prog) + `("PERL5LIB" ":" prefix + (,(string-append out "/lib/perl5/site_perl"))))) + '("rsem-calculate-expression" + "rsem-control-fdr" + "rsem-generate-data-matrix" + "rsem-generate-ngvector" + "rsem-plot-transcript-wiggles" + "rsem-prepare-reference" + "rsem-run-ebseq" + "rsem-run-prsem-testing-procedure"))) + #t))))) (inputs `(("boost" ,boost) - ("ncurses" ,ncurses) ("r-minimal" ,r-minimal) ("perl" ,perl) - ("samtools" ,samtools-0.1) + ("htslib" ,htslib-1.3) ("zlib" ,zlib))) (home-page "http://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") |