diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2f4355d87..4fd9459350 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -31,6 +31,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages file) #:use-module (gnu packages java) + #:use-module (gnu packages linux) #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) @@ -1219,6 +1220,81 @@ Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.") (license license:public-domain))) +(define-public sra-tools + (package + (name "sra-tools") + (version "2.4.5-5") + (source + (origin + (method url-fetch) + (uri + (string-append "https://github.com/ncbi/sra-tools/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-build? #f ; not supported + #:tests? #f ; no "check" target + #:phases + (alist-replace + 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; The build system expects a directory containing the sources and + ;; raw build output of ncbi-vdb, including files that are not + ;; installed. Since we are building against an installed version of + ;; ncbi-vdb, the following modifications are needed. + (substitute* "setup/konfigure.perl" + ;; Make the configure script look for the "ilib" directory of + ;; "ncbi-vdb" without first checking for the existence of a + ;; matching library in its "lib" directory. + (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") + "my $f = File::Spec->catdir($ilibdir, $ilib);") + ;; Look for interface libraries in ncbi-vdb's "ilib" directory. + (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") + "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* + "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" (assoc-ref outputs "out")) + (string-append "--debug") + (string-append "--with-fuse-prefix=" + (assoc-ref inputs "fuse")) + (string-append "--with-magic-prefix=" + (assoc-ref inputs "libmagic")) + ;; TODO: building with libxml2 fails with linker errors + ;; (string-append "--with-xml2-prefix=" + ;; (assoc-ref inputs "libxml2")) + (string-append "--with-ncbi-vdb-sources=" + (assoc-ref inputs "ncbi-vdb")) + (string-append "--with-ncbi-vdb-build=" + (assoc-ref inputs "ncbi-vdb")) + (string-append "--with-ngs-sdk-prefix=" + (assoc-ref inputs "ngs-sdk")) + (string-append "--with-hdf5-prefix=" + (assoc-ref inputs "hdf5"))))) + %standard-phases))) + (native-inputs `(("perl" ,perl))) + (inputs + `(("ngs-sdk" ,ngs-sdk) + ("ncbi-vdb" ,ncbi-vdb) + ("libmagic" ,file) + ("fuse" ,fuse) + ("hdf5" ,hdf5) + ("zlib" ,zlib))) + (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") + (synopsis "Tools and libraries for reading and writing sequencing data") + (description + "The SRA Toolkit from NCBI is a collection of tools and libraries for +reading of sequencing files from the Sequence Read Archive (SRA) database and +writing files into the .sra format.") + (license license:public-domain))) + (define-public seqan (package (name "seqan") |