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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-06-23 10:54:00 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-07-08 17:05:00 +0200
commit56e373ef75d161325d4878f8cfaafffa7dba24a5 (patch)
tree61eab520e4526306959992ba84b174af3e198620 /gnu/packages/bioinformatics.scm
parent5bdda30b32676528bcfa0a169c30237fabaa4607 (diff)
downloadguix-56e373ef75d161325d4878f8cfaafffa7dba24a5.tar
guix-56e373ef75d161325d4878f8cfaafffa7dba24a5.tar.gz
gnu: Add preseq.
* gnu/packages/bioinformatics.scm (preseq): New variable. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file. * gnu-system.am (dist_patch_DATA): Add them.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm56
1 files changed, 56 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f6349cfb8f..2b7f78be34 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2087,6 +2087,62 @@ subsequent visualization, annotation and storage of results.")
;; LGPLv2.1+
(license (list license:gpl2 license:lgpl2.1+))))
+(define-public preseq
+ (package
+ (name "preseq")
+ (version "1.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append "http://smithlabresearch.org/downloads/preseq-"
+ version ".tar.bz2"))
+ (sha256
+ (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+ (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
+ (search-patch "preseq-1.0.2-link-with-libbam.patch")))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled samtools.
+ '(delete-file-recursively "preseq-master/samtools"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'unpack 'enter-dir
+ (lambda _
+ (chdir "preseq-master")
+ #t))
+ (add-after
+ 'unpack 'use-samtools-headers
+ (lambda _
+ (substitute* '("smithlab_cpp/SAM.cpp"
+ "smithlab_cpp/SAM.hpp")
+ (("sam.h") "samtools/sam.h"))
+ #t))
+ (delete 'configure))
+ #:make-flags (list (string-append "PREFIX="
+ (assoc-ref %outputs "out"))
+ (string-append "LIBBAM="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/libbam.a"))))
+ (inputs
+ `(("gsl" ,gsl)
+ ("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "http://smithlabresearch.org/software/preseq/")
+ (synopsis "Program for analyzing library complexity")
+ (description
+ "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+ (license license:gpl3+)))
+
(define-public sra-tools
(package
(name "sra-tools")