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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-05-21 15:43:25 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-05-22 13:14:29 +0200
commit66e3eff1e31c4483aeb7a96ada8ea378fdc49e51 (patch)
tree7d0e2423fd89742829703f327e38394a1786c43e /gnu/packages/bioinformatics.scm
parent21461f27e7f2deef243ab4a4b6f04653e2d21e62 (diff)
gnu: Add rsem.
* gnu/packages/bioinformatics.scm (rsem): New variable. * gnu/packages/patches/rsem-makefile.patch: New file.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm78
1 files changed, 78 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c5a5c2eeb..b29ca67dbd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1013,6 +1013,84 @@ files and writing bioinformatics applications.")
generated using the PacBio Iso-Seq protocol.")
(license license:bsd-3))))
+(define-public rsem
+ (package
+ (name "rsem")
+ (version "1.2.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
+ (patches (list (search-patch "rsem-makefile.patch")))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; remove bundled copy of boost
+ (delete-file-recursively "boost")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #: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))
+ (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)
+ (copy-file file
+ (string-append bin (basename file))))
+ (find-files "." "rsem-.*"))
+ (copy-file "rsem_perl_utils.pm"
+ (string-append perl "/rsem_perl_utils.pm")))
+ #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)))))
+ (inputs
+ `(("boost" ,boost)
+ ("ncurses" ,ncurses)
+ ("r" ,r)
+ ("perl" ,perl)
+ ("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "http://deweylab.biostat.wisc.edu/rsem/")
+ (synopsis "Estimate gene expression levels from RNA-Seq data")
+ (description
+ "RSEM is a software package for estimating gene and isoform expression
+levels from RNA-Seq data. The RSEM package provides a user-friendly
+interface, supports threads for parallel computation of the EM algorithm,
+single-end and paired-end read data, quality scores, variable-length reads and
+RSPD estimation. In addition, it provides posterior mean and 95% credibility
+interval estimates for expression levels. For visualization, it can generate
+BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
+ (license license:gpl3+)))
+
(define-public rseqc
(package
(name "rseqc")