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-rw-r--r--gnu/packages/bioinformatics.scm52
1 files changed, 29 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3f1e6b3188..a9e0264369 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15159,11 +15159,20 @@ manipulations on VCF files.")
(sha256
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
(arguments
- `(#:tests? #f ; TODO: Re-enable when we have grep with perl support.
+ `(#:make-flags
+ (list "CC=gcc"
+ (string-append "BAMTOOLS_ROOT="
+ (assoc-ref %build-inputs "bamtools")))
#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "test/t/01_call_variants.t"
+ (("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
+ "grep -E ' (500|11000|1000)$'"))
+ #t))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
@@ -15184,32 +15193,29 @@ manipulations on VCF files.")
(unpack "tabixpp-src" "vcflib/tabixpp")
(unpack "test-simple-bash-src" "test/test-simple-bash")
(unpack "bash-tap-src" "test/bash-tap")))))
- (add-after 'unpack-submodule-sources 'fix-makefile
- (lambda* (#:key inputs #:allow-other-keys)
+ (add-after 'unpack-submodule-sources 'fix-makefiles
+ (lambda _
;; We don't have the .git folder to get the version tag from.
- (substitute* '("vcflib/Makefile")
- (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version)))))
- (replace 'build
+ (substitute* "vcflib/Makefile"
+ (("^GIT_VERSION.*")
+ (string-append "GIT_VERSION = v" ,version)))
+ (substitute* "src/Makefile"
+ (("-I\\$\\(BAMTOOLS_ROOT\\)/src")
+ "-I$(BAMTOOLS_ROOT)/include/bamtools"))
+ #t))
+ (add-before 'build 'build-tabixpp-and-vcflib
(lambda* (#:key inputs make-flags #:allow-other-keys)
(with-directory-excursion "vcflib"
(with-directory-excursion "tabixpp"
- (pk "Compile tabixpp before compiling the main project.")
- (let ((htslib-ref (assoc-ref inputs "htslib")))
- (invoke "make" "HTS_HEADERS="
- (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
- (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))
- (pk "Compile vcflib before compiling the main project.")
- (invoke "make" "CC=gcc"
- (string-append "CFLAGS=\"" "-Itabixpp "
- "-I" (assoc-ref inputs "htslib") "/include " "\"")
- "all"))
- (pk "Compile the main project.")
- (with-directory-excursion "src"
- (substitute* "Makefile"
- (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools"))
- (invoke "make"
- (string-append "BAMTOOLS_ROOT="
- (assoc-ref inputs "bamtools"))))))
+ (apply invoke "make"
+ (string-append "HTS_LIB="
+ (assoc-ref inputs "htslib")
+ "/lib/libhts.a")
+ make-flags))
+ (apply invoke "make"
+ (string-append "CFLAGS=-Itabixpp")
+ "all"
+ make-flags))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))