gnu: vcflib: Fix generated pkg-config file.

* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b14e76..39611d2 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15209,18 +15209,18 @@ library automatically handles index file generation and use.")
              (let* ((out (assoc-ref outputs "out"))
                     (pkgconfig (string-append out "/lib/pkgconfig")))
                (mkdir-p pkgconfig)
-               (with-output-to-file (string-append pkgconfig "/libvcflib.pc")
+               (with-output-to-file (string-append pkgconfig "/vcflib.pc")
                  (lambda _
                    (format #t "prefix=~a~@
                            exec_prefix=${prefix}~@
                            libdir=${exec_prefix}/lib~@
                            includedir=${prefix}/include~@
                            ~@
-                           Name: libvcflib~@
+                           Name: vcflib~@
                            Version: ~a~@
-                           Requires: smithwaterman, fastahack~@
+                           Requires: smithwaterman, fastahack, tabixpp~@
                            Description: C++ library for parsing and manipulating VCF files~@
-                           Libs: -L${libdir} -llibvcflib~@
+                           Libs: -L${libdir} -lvcflib~@
                            Cflags: -I${includedir}~%"
                            out ,version)))
                  #t))))))

diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
index 7e84666..9886de1 100644 (file)
--- a/gnu/packages/patches/freebayes-devendor-deps.patch
+++ b/gnu/packages/patches/freebayes-devendor-deps.patch
@@ -23,7 +23,7 @@ index f6bf242..bded4af 100644
 +tabixpp_dep = dependency('tabixpp', required : false)
 +fastahack_dep = dependency('fastahack', required : false)
 +smithwaterman_dep = dependency('smithwaterman', required : false)
-+vcflib_dep = dependency('libvcflib', required: false)
++vcflib_dep = dependency('vcflib', required: false)
  thread_dep = dependency('threads')
  
  if htslib_dep.found()