diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
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"))) |