diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 136 |
1 files changed, 134 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1766855c93..b64dab73cd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22,6 +22,7 @@ #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages base) @@ -34,6 +35,63 @@ #: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") @@ -197,8 +255,15 @@ Illumina, Roche 454, and the SOLiD platform.") "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5")))) (build-system gnu-build-system) (arguments - '(#:tests? #f ;no check target - #:make-flags '("allall") + `(#:tests? #f ;no check target + #:make-flags '("allall" + ;; Disable unsupported `popcnt' instructions on + ;; architectures other than x86_64 + ,@(if (string-prefix? "x86_64" + (or (%current-target-system) + (%current-system))) + '() + '("POPCNT_CAPABILITY=0"))) #:phases (alist-replace 'unpack @@ -246,6 +311,73 @@ several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.") (license license:gpl3+))) +(define-public htseq + (package + (name "htseq") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" + version ".tar.gz")) + (sha256 + (base32 + "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; only Python 2 is supported + (inputs + `(("python-numpy" ,python2-numpy) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://www-huber.embl.de/users/anders/HTSeq/") + (synopsis "Analysing high-throughput sequencing data with Python") + (description + "HTSeq is a Python package that provides infrastructure to process data +from high-throughput sequencing assays.") + (license license:gpl3+))) + +(define-public rseqc + (package + (name "rseqc") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/rseqc/" + version "/RSeQC-" version ".tar.gz")) + (sha256 + (base32 "09rf0x9d6apjja5l01cgprj7vigpw6kiqhy34ibwwlxil0db0ri4")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled copy of pysam + (delete-file-recursively "lib/pysam") + (substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") "") + ;; do not use bundled copy of pysam + (("^have_pysam = False") "have_pysam = True")))))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) + (inputs + `(("python-cython" ,python2-cython) + ("python-pysam" ,python2-pysam) + ("python-numpy" ,python2-numpy) + ("python-setuptools" ,python2-setuptools) + ("zlib" ,zlib))) + (native-inputs + `(("python-nose" ,python2-nose))) + (home-page "http://rseqc.sourceforge.net/") + (synopsis "RNA-seq quality control package") + (description + "RSeQC provides a number of modules that can comprehensively evaluate +high throughput sequence data, especially RNA-seq data. Some basic modules +inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, +while RNA-seq specific modules evaluate sequencing saturation, mapped reads +distribution, coverage uniformity, strand specificity, etc.") + (license license:gpl3+))) + (define-public samtools (package (name "samtools") |