@@ -210,85 +210,6 @@ (define-public aragorn
structure of the predicted RNA.")
(license license:gpl2)))
-(define-public bamm
- (package
- (name "bamm")
- (version "1.7.3")
- (source (origin
- (method git-fetch)
- ;; BamM is not available on pypi.
- (uri (git-reference
- (url "https://github.com/Ecogenomics/BamM")
- (commit version)
- (recursive? #t)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
- (modules '((guix build utils)))
- (snippet
- `(begin
- ;; Delete bundled htslib.
- (delete-file-recursively "c/htslib-1.3.1")))))
- (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 #$(this-package-input "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")))
- (for-each make-file-writable (find-files "." ".*"))
- ;; Use autogen so that 'configure' works.
- (substitute* "autogen.sh" (("/bin/sh") sh))
- (setenv "CONFIG_SHELL" sh)
- (invoke "./autogen.sh")))))
- (delete 'build) ;the build loops otherwise
- (replace 'check
- (lambda _
- ;; 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 ...
- (invoke "nosetests")))
- (add-after 'install 'wrap-executable
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (path (getenv "PATH"))
- (pythonpath (getenv "GUIX_PYTHONPATH")))
- (wrap-program (string-append out "/bin/bamm")
- `("PATH" ":" prefix (,path))
- `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))))))))
- (native-inputs
- (list autoconf
- automake
- libtool
- zlib
- python2-nose
- python2-pysam))
- (inputs
- (list htslib-1.3 ; At least one test fails on htslib-1.4+.
- samtools
- bwa
- grep
- sed
- coreutils))
- (propagated-inputs
- (list python2-numpy))
- (home-page "https://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")