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-rw-r--r--gn/packages/sambamba.scm48
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