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-rw-r--r--gnu/packages/bioinformatics.scm93
1 files changed, 93 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b206f3344d..f0dc45a8ce 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -136,6 +136,99 @@ tRNA consensus sequences and RNA structure. It also outputs the secondary
structure of the predicted RNA.")
(license license:gpl2)))
+(define-public bamm
+ (package
+ (name "bamm")
+ (version "1.7.2a")
+ (source (origin
+ (method url-fetch)
+ ;; BamM is not available on pypi.
+ (uri (string-append
+ "https://github.com/Ecogenomics/BamM/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0nb20yml39f8fh0cahpjywsl91irh9yskig549c17xkrkl74czsq"))
+ (modules '((guix build utils)))
+ (snippet
+ `(begin
+ ;; Delete bundled htslib.
+ (delete-file-recursively "c/htslib-1.3.1")
+ #t))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; BamM is Python 2 only.
+ ;; Do not use bundled libhts. Do use the bundled libcfu because it has
+ ;; been modified from its original form.
+ #:configure-flags
+ (let ((htslib (assoc-ref %build-inputs "htslib")))
+ (list "--with-libhts-lib" (string-append htslib "/lib")
+ "--with-libhts-inc" (string-append htslib "/include/htslib")))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'autogen
+ (lambda _
+ (with-directory-excursion "c"
+ (let ((sh (which "sh")))
+ ;; Use autogen so that 'configure' works.
+ (substitute* "autogen.sh" (("/bin/sh") sh))
+ (setenv "CONFIG_SHELL" sh)
+ (substitute* "configure" (("/bin/sh") sh))
+ (zero? (system* "./autogen.sh"))))))
+ (delete 'build)
+ ;; Run tests after installation so compilation only happens once.
+ (delete 'check)
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (path (getenv "PATH")))
+ (wrap-program (string-append out "/bin/bamm")
+ `("PATH" ":" prefix (,path))))
+ #t))
+ (add-after 'wrap-executable 'post-install-check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PATH"
+ (string-append (assoc-ref outputs "out")
+ "/bin:"
+ (getenv "PATH")))
+ (setenv "PYTHONPATH"
+ (string-append
+ (assoc-ref outputs "out")
+ "/lib/python"
+ (string-take (string-take-right
+ (assoc-ref inputs "python") 5) 3)
+ "/site-packages:"
+ (getenv "PYTHONPATH")))
+ ;; There are 2 errors printed, but they are safe to ignore:
+ ;; 1) [E::hts_open_format] fail to open file ...
+ ;; 2) samtools view: failed to open ...
+ (zero? (system* "nosetests")))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("zlib" ,zlib)
+ ("python-nose" ,python2-nose)
+ ("python-pysam" ,python2-pysam)
+ ("python-setuptools" ,python2-setuptools)))
+ (inputs
+ `(("htslib" ,htslib)
+ ("samtools" ,samtools)
+ ("bwa" ,bwa)
+ ("grep" ,grep)
+ ("sed" ,sed)
+ ("coreutils" ,coreutils)))
+ (propagated-inputs
+ `(("python-numpy" ,python2-numpy)))
+ (home-page "http://ecogenomics.github.io/BamM/")
+ (synopsis "Metagenomics-focused BAM file manipulator")
+ (description
+ "BamM is a C library, wrapped in python, to efficiently generate and
+parse BAM files, specifically for the analysis of metagenomic data. For
+instance, it implements several methods to assess contig-wise read coverage.")
+ (license license:lgpl3+)))
+
(define-public bamtools
(package
(name "bamtools")