diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 138 |
1 files changed, 138 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8ed871003a..1214a0b708 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -27,6 +27,7 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages java) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -237,6 +238,53 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public bwa + (package + (name "bwa") + (version "0.7.12") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bio-bwa/bwa-" + version ".tar.bz2")) + (sha256 + (base32 + "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:phases + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append + (assoc-ref outputs "out") "/bin")) + (doc (string-append + (assoc-ref outputs "out") "/share/doc/bwa")) + (man (string-append + (assoc-ref outputs "out") "/share/man/man1"))) + (mkdir-p bin) + (mkdir-p doc) + (mkdir-p man) + (copy-file "bwa" (string-append bin "/bwa")) + (copy-file "README.md" (string-append doc "/README.md")) + (copy-file "bwa.1" (string-append man "/bwa.1")))) + ;; no "configure" script + (alist-delete 'configure %standard-phases)))) + (inputs `(("zlib" ,zlib))) + (home-page "http://bio-bwa.sourceforge.net/") + (synopsis "Burrows-Wheeler sequence aligner") + (description + "BWA is a software package for mapping low-divergent sequences against a +large reference genome, such as the human genome. It consists of three +algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is +designed for Illumina sequence reads up to 100bp, while the rest two for +longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar +features such as long-read support and split alignment, but BWA-MEM, which is +the latest, is generally recommended for high-quality queries as it is faster +and more accurate. BWA-MEM also has better performance than BWA-backtrack for +70-100bp Illumina reads.") + (license license:gpl3+))) + (define-public clipper (package (name "clipper") @@ -446,6 +494,51 @@ particular, reads spanning multiple exons.") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public htsjdk + (package + (name "htsjdk") + (version "1.129") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htsjdk/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) + (modules '((guix build utils))) + ;; remove build dependency on git + (snippet '(substitute* "build.xml" + (("failifexecutionfails=\"true\"") + "failifexecutionfails=\"false\""))))) + (build-system gnu-build-system) + (arguments + `(#:modules ((srfi srfi-1) + (guix build gnu-build-system) + (guix build utils)) + #:phases (alist-replace + 'build + (lambda _ + (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk")) + (zero? (system* "ant" "all" + (string-append "-Ddist=" + (assoc-ref %outputs "out") + "/share/java/htsjdk/")))) + (fold alist-delete %standard-phases + '(configure install check))))) + (native-inputs + `(("ant" ,ant) + ("jdk" ,icedtea6 "jdk"))) + (home-page "http://samtools.github.io/htsjdk/") + (synopsis "Java API for high-throughput sequencing data (HTS) formats") + (description + "HTSJDK is an implementation of a unified Java library for accessing +common file formats, such as SAM and VCF, used for high-throughput +sequencing (HTS) data. There are also an number of useful utilities for +manipulating HTS data.") + (license license:expat))) + (define-public macs (package (name "macs") @@ -477,6 +570,51 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) +(define-public miso + (package + (name "miso") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (string-append + "http://pypi.python.org/packages/source/m/misopy/misopy-" + version ".tar.gz")) + (sha256 + (base32 + "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w")) + (modules '((guix build utils))) + ;; use "gcc" instead of "cc" for compilation + (snippet + '(substitute* "setup.py" + (("^defines") + "cc.set_executables( +compiler='gcc', +compiler_so='gcc', +linker_exe='gcc', +linker_so='gcc -shared'); defines"))))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; only Python 2 is supported + #:tests? #f)) ; no "test" target + (inputs + `(("samtools" ,samtools) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-scipy" ,python2-scipy) + ("python-matplotlib" ,python2-matplotlib))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://genes.mit.edu/burgelab/miso/index.html") + (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") + (description + "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates +the expression level of alternatively spliced genes from RNA-Seq data, and +identifies differentially regulated isoforms or exons across samples. By +modeling the generative process by which reads are produced from isoforms in +RNA-Seq, the MISO model uses Bayesian inference to compute the probability +that a read originated from a particular isoform.") + (license license:gpl2))) + (define-public rseqc (package (name "rseqc") |