diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/sambamba.scm | 48 |
1 files changed, 47 insertions, 1 deletions
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm index cb10355..31ec54f 100644 --- a/gn/packages/sambamba.scm +++ b/gn/packages/sambamba.scm @@ -10,14 +10,60 @@ #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) ; for samtools in sambamba #:use-module (gnu packages compression) + #:use-module (gnu packages curl) + #:use-module (gnu packages dlang) #:use-module (gnu packages gcc) #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages ruby) - #:use-module (gnu packages dlang) + #:use-module (gnu packages tls) #:use-module (gn packages shell) #:use-module (srfi srfi-1)) + +(define-public htslib + (package + (name "htslib") + (version "1.11-codecs") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng")))) + (build-system gnu-build-system) + ;; Let htslib translate "gs://" and "s3://" to regular https links with + ;; "--enable-gcs" and "--enable-s3". For these options to work, we also + ;; need to set "--enable-libcurl". + (arguments + `(#:configure-flags '("--enable-gcs" + "--enable-libcurl" + "--enable-s3" + "--enable-lzma" + "--enable-bz2"))) + (inputs + `(("curl" ,curl) + ("openssl" ,openssl) + ("xz" ,xz) ; for liblzma codec + ("bzip2" ,bzip2))) ; for libz2 codec + ;; This is referred to in the pkg-config file as a required library. + (propagated-inputs + `(("zlib" ,zlib))) + (native-inputs + `(("perl" ,perl))) + (home-page "https://www.htslib.org") + (synopsis "C library for reading/writing high-throughput sequencing data") + (description + "HTSlib is a C library for reading/writing high-throughput sequencing +data. It also provides the @command{bgzip}, @command{htsfile}, and +@command{tabix} utilities.") + ;; Files under cram/ are released under the modified BSD license; + ;; the rest is released under the Expat license + (license (list license:expat license:bsd-3)))) + + (define-public sambamba (let ((commit "7cff06533b539a99b4e0db681fb573214d63aae2")) (package |