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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 93 |
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") |