diff options
| -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))) |