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gnu: sra-tools: Update to 2.10.6.

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* 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.
This commit is contained in:
Ricardo Wurmus 2020-05-19 12:39:22 +02:00
parent 68de995674
commit 9dc50c8c47
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1 changed files with 13 additions and 8 deletions
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21
gnu/packages/bioinformatics.scm
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@ -6148,7 +6148,7 @@ (define-public python2-screed
(define-public sra-tools (define-public sra-tools
(package (package
(name "sra-tools") (name "sra-tools")
(version "2.9.6") (version "2.10.6")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -6158,11 +6158,11 @@ (define-public sra-tools
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy")))) "1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:parallel-build? #f ; not supported `(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target #:tests? #f ; no "check" target
#:make-flags #:make-flags
(list (string-append "DEFAULT_CRT=" (list (string-append "DEFAULT_CRT="
(assoc-ref %build-inputs "ncbi-vdb") (assoc-ref %build-inputs "ncbi-vdb")
@ -6205,6 +6205,9 @@ (define-public sra-tools
;; Dynamic linking ;; Dynamic linking
(substitute* "tools/copycat/Makefile" (substitute* "tools/copycat/Makefile"
(("smagic-static") "lmagic")) (("smagic-static") "lmagic"))
(substitute* "tools/driver-tool/utf8proc/Makefile"
(("CC\\?=gcc") "myCC=gcc")
(("\\(CC\\)") "(myCC)"))
;; The 'configure' script doesn't recognize things like ;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'. ;; '--enable-fast-install'.
@ -6217,8 +6220,9 @@ (define-public sra-tools
(string-append "--with-magic-prefix=" (string-append "--with-magic-prefix="
(assoc-ref inputs "libmagic")) (assoc-ref inputs "libmagic"))
;; TODO: building with libxml2 fails with linker errors ;; 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=" (string-append "--with-ncbi-vdb-sources="
(assoc-ref inputs "ncbi-vdb")) (assoc-ref inputs "ncbi-vdb"))
(string-append "--with-ncbi-vdb-build=" (string-append "--with-ncbi-vdb-build="
@ -6234,8 +6238,9 @@ (define-public sra-tools
("ncbi-vdb" ,ncbi-vdb) ("ncbi-vdb" ,ncbi-vdb)
("libmagic" ,file) ("libmagic" ,file)
("fuse" ,fuse) ("fuse" ,fuse)
("hdf5" ,hdf5) ("hdf5" ,hdf5-1.10)
("zlib" ,zlib))) ("zlib" ,zlib)
("python" ,python-wrapper)))
(home-page (home-page
"https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
(synopsis "Tools and libraries for reading and writing sequencing data") (synopsis "Tools and libraries for reading and writing sequencing data")