diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 |
1 files changed, 17 insertions, 12 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32b795948b..a738aa51a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5723,7 +5723,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "2.9.6") + (version "2.10.5") (source (origin (method git-fetch) (uri (git-reference @@ -5732,7 +5732,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (file-name (git-file-name name version)) (sha256 (base32 - "0d5k5kabgl15as37kj9x65xc92j4gcqms86hvihw3yb6wag0r0q3")))) + "1ix51c25hjn57w93qmwzw80xh2i34wx8j2hn7szh8p6w8i3az5qa")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5789,7 +5789,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.9.6") + (version "2.10.6") (source (origin (method git-fetch) (uri (git-reference @@ -5798,7 +5798,7 @@ simultaneously.") (file-name (git-file-name name version)) (sha256 (base32 - "0knkj1sq34hlivgv5qd6jlczqrs3ldmfgn6vbbw7p4mqxvb9mirk")))) + "0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -6148,7 +6148,7 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.9.6") + (version "2.10.6") (source (origin (method git-fetch) @@ -6158,11 +6158,11 @@ sequence itself can be retrieved from these databases.") (file-name (git-file-name name version)) (sha256 (base32 - "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy")))) + "1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf")))) (build-system gnu-build-system) (arguments - `(#:parallel-build? #f ; not supported - #:tests? #f ; no "check" target + `(#:parallel-build? #f ; not supported + #:tests? #f ; no "check" target #:make-flags (list (string-append "DEFAULT_CRT=" (assoc-ref %build-inputs "ncbi-vdb") @@ -6205,6 +6205,9 @@ sequence itself can be retrieved from these databases.") ;; Dynamic linking (substitute* "tools/copycat/Makefile" (("smagic-static") "lmagic")) + (substitute* "tools/driver-tool/utf8proc/Makefile" + (("CC\\?=gcc") "myCC=gcc") + (("\\(CC\\)") "(myCC)")) ;; The 'configure' script doesn't recognize things like ;; '--enable-fast-install'. @@ -6217,8 +6220,9 @@ sequence itself can be retrieved from these databases.") (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-xml2-prefix=" + (assoc-ref inputs "libxml2")) (string-append "--with-ncbi-vdb-sources=" (assoc-ref inputs "ncbi-vdb")) (string-append "--with-ncbi-vdb-build=" @@ -6234,8 +6238,9 @@ sequence itself can be retrieved from these databases.") ("ncbi-vdb" ,ncbi-vdb) ("libmagic" ,file) ("fuse" ,fuse) - ("hdf5" ,hdf5) - ("zlib" ,zlib))) + ("hdf5" ,hdf5-1.10) + ("zlib" ,zlib) + ("python" ,python-wrapper))) (home-page "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") (synopsis "Tools and libraries for reading and writing sequencing data") |