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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b14b7d4caf..b3aedec63f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2722,6 +2722,69 @@ several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.") (license license:gpl3+))) +(define-public hisat2 + (package + (name "hisat2") + (version "2.0.5") + (source + (origin + (method url-fetch) + ;; FIXME: a better source URL is + ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" + ;; "/downloads/hisat2-" version "-source.zip") + ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g" + ;; but it is currently unavailable. + (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz") + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:make-flags (list "CC=gcc" "CXX=g++" "allall") + #:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-deterministic + (lambda _ + (substitute* "Makefile" + (("`date`") "0")) + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin/")) + (doc (string-append out "/share/doc/hisat2/"))) + (for-each + (cut install-file <> bin) + (find-files "." + "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) + (mkdir-p doc) + (install-file "doc/manual.inc.html" doc)) + #t))))) + (native-inputs + `(("unzip" ,unzip) ; needed for archive from ftp + ("perl" ,perl) + ("pandoc" ,ghc-pandoc))) ; for documentation + (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml") + (synopsis "Graph-based alignment of genomic sequencing reads") + (description "HISAT2 is a fast and sensitive alignment program for mapping +next-generation sequencing reads (both DNA and RNA) to a population of human +genomes (as well as to a single reference genome). In addition to using one +global @dfn{graph FM} (GFM) index that represents a population of human +genomes, HISAT2 uses a large set of small GFM indexes that collectively cover +the whole genome. These small indexes, combined with several alignment +strategies, enable rapid and accurate alignment of sequencing reads. This new +indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") + ;; HISAT2 contains files from Bowtie2, which is released under + ;; GPLv2 or later. The HISAT2 source files are released under + ;; GPLv3 or later. + (license license:gpl3+))) + (define-public hmmer (package (name "hmmer") |