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gnu: freebayes: Simplify and enable tests. 

* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set
make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles"
phase; move build of tabixpp and vcflib to separate phase
"build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build"
phase.
This commit is contained in:
Ricardo Wurmus 2019-08-09 12:06:59 +02:00
parent 7cd98e868e
commit c2847323d8
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GPG Key ID: 197A5888235FACAC
1 changed files with 29 additions and 23 deletions
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@ -15159,11 +15159,20 @@ manipulations on VCF files.")
(sha256 (sha256
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
(arguments (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" #:test-target "test"
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) (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)$'"))
#t))
(add-after 'unpack 'unpack-submodule-sources (add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target) (let ((unpack (lambda (source target)
@ -15184,32 +15193,29 @@ manipulations on VCF files.")
(unpack "tabixpp-src" "vcflib/tabixpp") (unpack "tabixpp-src" "vcflib/tabixpp")
(unpack "test-simple-bash-src" "test/test-simple-bash") (unpack "test-simple-bash-src" "test/test-simple-bash")
(unpack "bash-tap-src" "test/bash-tap"))))) (unpack "bash-tap-src" "test/bash-tap")))))
(add-after 'unpack-submodule-sources 'fix-makefile (add-after 'unpack-submodule-sources 'fix-makefiles
(lambda* (#:key inputs #:allow-other-keys) (lambda _
;; We don't have the .git folder to get the version tag from. ;; We don't have the .git folder to get the version tag from.
(substitute* '("vcflib/Makefile") (substitute* "vcflib/Makefile"
(("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) (("^GIT_VERSION.*")
(replace 'build (string-append "GIT_VERSION = v" ,version)))
(substitute* "src/Makefile"
(("-I\\$\\(BAMTOOLS_ROOT\\)/src")
"-I$(BAMTOOLS_ROOT)/include/bamtools"))
#t))
(add-before 'build 'build-tabixpp-and-vcflib
(lambda* (#:key inputs make-flags #:allow-other-keys) (lambda* (#:key inputs make-flags #:allow-other-keys)
(with-directory-excursion "vcflib" (with-directory-excursion "vcflib"
(with-directory-excursion "tabixpp" (with-directory-excursion "tabixpp"
(pk "Compile tabixpp before compiling the main project.") (apply invoke "make"
(let ((htslib-ref (assoc-ref inputs "htslib"))) (string-append "HTS_LIB="
(invoke "make" "HTS_HEADERS=" (assoc-ref inputs "htslib")
(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") "/lib/libhts.a")
(string-append "LIBPATH=-L. -L" htslib-ref "/include")))) make-flags))
(pk "Compile vcflib before compiling the main project.") (apply invoke "make"
(invoke "make" "CC=gcc" (string-append "CFLAGS=-Itabixpp")
(string-append "CFLAGS=\"" "-Itabixpp " "all"
"-I" (assoc-ref inputs "htslib") "/include " "\"") make-flags))))
"all"))
(pk "Compile the main project.")
(with-directory-excursion "src"
(substitute* "Makefile"
(("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools"))
(invoke "make"
(string-append "BAMTOOLS_ROOT="
(assoc-ref inputs "bamtools"))))))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (let ((bin (string-append (assoc-ref outputs "out") "/bin")))