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| author | Ricardo Wurmus <rekado@elephly.net> | 2020-05-19 12:39:22 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2020-05-19 12:42:01 +0200 |
| commit | 9dc50c8c4742811cb2ca953e075e0ea6e0c09213 (patch) | |
| tree | 2a09012a67cd2c7c99a69d0a0b5d2d7b852d8481 /gnu/packages/bioinformatics.scm | |
| parent | 68de9956749043bec425839c1154ad0ea64a4baa (diff) | |
| download | guix-patches-9dc50c8c4742811cb2ca953e075e0ea6e0c09213.tar guix-patches-9dc50c8c4742811cb2ca953e075e0ea6e0c09213.tar.gz | |
gnu: sra-tools: Update to 2.10.6.
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6.
[arguments]: Replace CC variable in utf8proc Makefile.
[inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 21 |
1 files changed, 13 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ad08b9db5..a738aa51a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |