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| author | Marius Bakke <mbakke@fastmail.com> | 2016-09-22 14:08:05 +0100 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-09-27 20:06:00 +1000 |
| commit | dff26b2363c1735e3d84e0dbd2b958760b08f848 (patch) | |
| tree | b270fc8951ef2797ba2288ac4c817b745aeb5eb5 | |
| parent | 397d463a12b719146ffe4f444f5f3e83cee4794e (diff) | |
| download | patches-dff26b2363c1735e3d84e0dbd2b958760b08f848.tar patches-dff26b2363c1735e3d84e0dbd2b958760b08f848.tar.gz | |
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.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 15 |
1 files changed, 13 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6e3218a26..3ca6fd6c34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1354,17 +1354,28 @@ multiple sequence alignments.") (uri (pypi-uri "pysam" version)) (sha256 (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) (arguments `(#:tests? #f ; tests are excluded in the manifest #:phases (modify-phases %standard-phases (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 "CFLAGS" "-D_CURSES_LIB=1") #t))))) + (propagated-inputs + `(("htslib" ,htslib))) ; Included from installed header files. (inputs `(("ncurses" ,ncurses) ("zlib" ,zlib))) |