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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 75837923e2..5bd668ee14 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -34,6 +34,63 @@ #:use-module (gnu packages vim) #:use-module (gnu packages zip)) +(define-public bedops + (package + (name "bedops") + (version "2.4.5") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/bedops/bedops/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f + #:make-flags (list (string-append "BINDIR=" %output "/bin")) + #:phases + (alist-cons-after + 'unpack 'unpack-tarballs + (lambda _ + ;; FIXME: Bedops includes tarballs of minimally patched upstream + ;; libraries jansson, zlib, and bzip2. We cannot just use stock + ;; libraries because at least one of the libraries (zlib) is + ;; patched to add a C++ function definition (deflateInit2cpp). + ;; Until the Bedops developers offer a way to link against system + ;; libraries we have to build the in-tree copies of these three + ;; libraries. + + ;; See upstream discussion: + ;; https://github.com/bedops/bedops/issues/124 + + ;; Unpack the tarballs to benefit from shebang patching. + (with-directory-excursion "third-party" + (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2")) + (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2")) + (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2")))) + ;; Disable unpacking of tarballs in Makefile. + (substitute* "system.mk/Makefile.linux" + (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") + (("\\./configure") "CONFIG_SHELL=bash ./configure")) + (substitute* "third-party/zlib-1.2.7/Makefile.in" + (("^SHELL=.*$") "SHELL=bash\n"))) + (alist-delete 'configure %standard-phases)))) + (home-page "https://github.com/bedops/bedops") + (synopsis "Tools for high-performance genomic feature operations") + (description + "BEDOPS is a suite of tools to address common questions raised in genomic +studies---mostly with regard to overlap and proximity relationships between +data sets. It aims to be scalable and flexible, facilitating the efficient +and accurate analysis and management of large-scale genomic data. + +BEDOPS provides tools that perform highly efficient and scalable Boolean and +other set operations, statistical calculations, archiving, conversion and +other management of genomic data of arbitrary scale. Tasks can be easily +split by chromosome for distributing whole-genome analyses across a +computational cluster.") + (license license:gpl2+))) + (define-public bedtools (package (name "bedtools") |