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gnu: python-pysam: Delete bundled htslib. 

* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
This commit is contained in:
Marius Bakke 2016-09-22 14:08:05 +01:00 committed by Ben Woodcroft
parent 397d463a12
commit dff26b2363
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1 changed files with 13 additions and 2 deletions
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@ -1354,17 +1354,28 @@ multiple sequence alignments.")
(uri (pypi-uri "pysam" version)) (uri (pypi-uri "pysam" version))
(sha256 (sha256
(base32 (base32
"1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn")))) "1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn"))
(modules '((guix build utils)))
(snippet
;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
'(delete-file-recursively "htslib"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:tests? #f ; tests are excluded in the manifest `(#:tests? #f ; tests are excluded in the manifest
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-before 'build 'set-flags (add-before 'build 'set-flags
(lambda _ (lambda* (#:key inputs #:allow-other-keys)
(setenv "HTSLIB_MODE" "external")
(setenv "HTSLIB_LIBRARY_DIR"
(string-append (assoc-ref inputs "htslib") "/lib"))
(setenv "HTSLIB_INCLUDE_DIR"
(string-append (assoc-ref inputs "htslib") "/include"))
(setenv "LDFLAGS" "-lncurses") (setenv "LDFLAGS" "-lncurses")
(setenv "CFLAGS" "-D_CURSES_LIB=1") (setenv "CFLAGS" "-D_CURSES_LIB=1")
#t))))) #t)))))
(propagated-inputs
`(("htslib" ,htslib))) ; Included from installed header files.
(inputs (inputs
`(("ncurses" ,ncurses) `(("ncurses" ,ncurses)
("zlib" ,zlib))) ("zlib" ,zlib)))