diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 77 |
1 files changed, 70 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ec4c44ef54..01c45fcc96 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -354,6 +354,28 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. (license (list license:gpl3+ license:expat)))) +(define-public bcftools-1.9 + (package (inherit bcftools) + (name "bcftools") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/samtools/bcftools/" + "releases/download/" + version "/bcftools-" version ".tar.bz2")) + (sha256 + (base32 + "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) + (build-system gnu-build-system) + (native-inputs + `(("htslib" ,htslib-1.9) + ("perl" ,perl))))) + (define-public bedops (package (name "bedops") @@ -437,7 +459,7 @@ computational cluster.") (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) + `(("samtools" ,samtools-1.9) ("zlib" ,zlib))) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") @@ -1955,7 +1977,7 @@ multiple sequence alignments.") ;; FIXME: tests keep timing out on some systems. (invoke "nosetests" "-v" "--processes" "1"))))))) (propagated-inputs - `(("htslib" ,htslib))) ; Included from installed header files. + `(("htslib" ,htslib-1.9))) ; Included from installed header files. (inputs `(("ncurses" ,ncurses) ("curl" ,curl) @@ -1963,8 +1985,8 @@ multiple sequence alignments.") (native-inputs `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. - ("samtools" ,samtools) - ("bcftools" ,bcftools) + ("samtools" ,samtools-1.9) + ("bcftools" ,bcftools-1.9) ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") @@ -4250,6 +4272,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public htslib-1.9 + (package (inherit htslib) + (name "htslib") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))))) + ;; This package should be removed once no packages rely upon it. (define htslib-1.3 (package @@ -5686,6 +5721,31 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) +(define-public samtools-1.9 + (package (inherit samtools) + (name "samtools") + (version "1.9") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/samtools/samtools/" + version "/samtools-" version ".tar.bz2")) + (sha256 + (base32 + "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) + (inputs + `(("htslib" ,htslib-1.9) + ("ncurses" ,ncurses) + ("perl" ,perl) + ("python" ,python) + ("zlib" ,zlib))))) + (define-public samtools-0.1 ;; This is the most recent version of the 0.1 line of samtools. The input ;; and output formats differ greatly from that used and produced by samtools @@ -15376,7 +15436,7 @@ patterns.") (define-public methyldackel (package (name "methyldackel") - (version "0.4.0") + (version "0.5.1") (source (origin (method git-fetch) (uri (git-reference @@ -15385,7 +15445,7 @@ patterns.") (file-name (git-file-name name version)) (sha256 (base32 - "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g")))) + "1sfhf2ap75qxpnmy1ifgmxqs18rq8mah9mcgkby73vc6h0sw99ws")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -15398,11 +15458,14 @@ patterns.") (replace 'configure (lambda* (#:key outputs #:allow-other-keys) (substitute* "Makefile" + (("-lhts ") "-lhts -lBigWig ") (("install MethylDackel \\$\\(prefix\\)" match) (string-append "install -d $(prefix); " match))) #t))))) (inputs - `(("htslib" ,htslib) + `(("curl" ,curl) ; XXX: needed by libbigwig + ("htslib" ,htslib-1.9) + ("libbigwig" ,libbigwig) ("zlib" ,zlib))) ;; Needed for tests (native-inputs |