06/09: gnu: python-pysam: Delete bundled htslib.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit dff26b2363c1735e3d84e0dbd2b958760b08f848
Author: Marius Bakke <address@hidden>
Date:   Thu Sep 22 14:08:05 2016 +0100

    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.
---
 gnu/packages/bioinformatics.scm |   15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a6e3218..3ca6fd6 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)))