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authorRicardo Wurmus <rekado@elephly.net>2020-05-19 12:39:22 +0200
committerRicardo Wurmus <rekado@elephly.net>2020-05-19 12:42:01 +0200
commit9dc50c8c4742811cb2ca953e075e0ea6e0c09213 (patch)
tree2a09012a67cd2c7c99a69d0a0b5d2d7b852d8481
parent68de9956749043bec425839c1154ad0ea64a4baa (diff)
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.
-rw-r--r--gnu/packages/bioinformatics.scm21
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")