diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 180 |
1 files changed, 89 insertions, 91 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 70134b34e2..990bdb28da 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2474,7 +2474,7 @@ package provides command line tools using the Bio++ library.") (define-public blast+ (package (name "blast+") - (version "2.11.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (string-append @@ -2482,7 +2482,7 @@ package provides command line tools using the Bio++ library.") version "/ncbi-blast-" version "+-src.tar.gz")) (sha256 (base32 - "0m0r9vkw631ky1za1wilsfk9k9spwqh22nkrb9a57rbwmrc1i3nq")) + "003mn7m4y306k7visv3in3ikfgm8m41z0jq9lyvz10iv1hdpyixz")) (modules '((guix build utils))) (snippet '(begin @@ -2518,103 +2518,101 @@ package provides command line tools using the Bio++ library.") (("cksum") "cksum >/dev/null")))))) (build-system gnu-build-system) (arguments - `(;; There are two(!) tests for this massive library, and both fail with - ;; "unparsable timing stats". - ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) - ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) - #:tests? #f - #:out-of-source? #t - #:parallel-build? #f ; not supported - #:phases - (modify-phases %standard-phases - (add-before 'configure 'set-HOME - ;; $HOME needs to be set at some point during the configure phase - (lambda _ (setenv "HOME" "/tmp") #t)) - (add-after 'unpack 'enter-dir - (lambda _ (chdir "c++") #t)) - (add-after 'enter-dir 'fix-build-system - (lambda _ - (define (which* cmd) - (cond ((string=? cmd "date") - ;; make call to "date" deterministic - "date -d @0") - ((which cmd) - => identity) - (else - (format (current-error-port) - "WARNING: Unable to find absolute path for ~s~%" - cmd) - #f))) + (list + ;; There are two(!) tests for this massive library, and both fail with + ;; "unparsable timing stats". + ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) + ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) + #:tests? #f + #:out-of-source? #t + #:parallel-build? #f ;not supported + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'set-HOME + ;; $HOME needs to be set at some point during the configure phase + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'enter-dir + (lambda _ (chdir "c++"))) + (add-after 'enter-dir 'fix-build-system + (lambda _ + (define (which* cmd) + (cond ((string=? cmd "date") + ;; make call to "date" deterministic + "date -d @0") + ((which cmd) + => identity) + (else + (format (current-error-port) + "WARNING: Unable to find absolute path for ~s~%" + cmd) + #false))) - ;; Rewrite hardcoded paths to various tools - (substitute* (append '("src/build-system/configure.ac" - "src/build-system/configure" - "src/build-system/helpers/run_with_lock.c" - "scripts/common/impl/if_diff.sh" - "scripts/common/impl/run_with_lock.sh" - "src/build-system/Makefile.configurables.real" - "src/build-system/Makefile.in.top" - "src/build-system/Makefile.meta.gmake=no" - "src/build-system/Makefile.meta.in" - "src/build-system/Makefile.meta_l" - "src/build-system/Makefile.meta_p" - "src/build-system/Makefile.meta_r" - "src/build-system/Makefile.mk.in" - "src/build-system/Makefile.requirements" - "src/build-system/Makefile.rules_with_autodep.in") - (find-files "scripts/common/check" "\\.sh$")) - (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) - (or (which* cmd) all))) + ;; Rewrite hardcoded paths to various tools + (substitute* (append '("src/build-system/configure.ac" + "src/build-system/configure" + "src/build-system/helpers/run_with_lock.c" + "scripts/common/impl/if_diff.sh" + "scripts/common/impl/run_with_lock.sh" + "src/build-system/Makefile.configurables.real" + "src/build-system/Makefile.in.top" + "src/build-system/Makefile.meta.gmake=no" + "src/build-system/Makefile.meta.in" + "src/build-system/Makefile.meta_l" + "src/build-system/Makefile.meta_p" + "src/build-system/Makefile.meta_r" + "src/build-system/Makefile.mk.in" + "src/build-system/Makefile.requirements" + "src/build-system/Makefile.rules_with_autodep.in") + (find-files "scripts/common/check" "\\.sh$")) + (("(/usr/bin/|/bin/)([a-z][-_.a-z]*(\\+\\+)?)" all dir cmd) + (or (which* cmd) all))) - (substitute* (find-files "src/build-system" "^config.*") - (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) - (("^PATH=.*") "")) + (substitute* (find-files "src/build-system" "^config.*") + (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) + (("^PATH=.*") "")) - ;; rewrite "/var/tmp" in check script - (substitute* "scripts/common/check/check_make_unix.sh" - (("/var/tmp") "/tmp")) + ;; rewrite "/var/tmp" in check script + (substitute* "scripts/common/check/check_make_unix.sh" + (("/var/tmp") "/tmp")) - ;; do not reset PATH - (substitute* (find-files "scripts/common/impl/" "\\.sh$") - (("^ *PATH=.*") "") - (("action=/bin/") "action=") - (("export PATH") ":")) - #t)) - (replace 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (lib (string-append (assoc-ref outputs "lib") "/lib")) - (include (string-append (assoc-ref outputs "include") - "/include/ncbi-tools++"))) - ;; The 'configure' script doesn't recognize things like - ;; '--enable-fast-install'. - (invoke "./configure.orig" - (string-append "--with-build-root=" (getcwd) "/build") - (string-append "--prefix=" out) - (string-append "--libdir=" lib) - (string-append "--includedir=" include) - (string-append "--with-bz2=" - (assoc-ref inputs "bzip2")) - (string-append "--with-z=" - (assoc-ref inputs "zlib")) - (string-append "--with-pcre=" - (assoc-ref inputs "pcre")) - ;; Each library is built twice by default, once - ;; with "-static" in its name, and again - ;; without. - "--without-static" - "--with-dll") - #t)))))) + ;; do not reset PATH + (substitute* (find-files "scripts/common/impl/" "\\.sh$") + (("^ *PATH=.*") "") + (("action=/bin/") "action=") + (("export PATH") ":")))) + (replace 'configure + (lambda _ + (let ((lib (string-append #$output:lib "/lib")) + (include (string-append #$output:include + "/include/ncbi-tools++"))) + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (invoke "./configure.orig" + (string-append "--with-build-root=" (getcwd) "/build") + (string-append "--prefix=" #$output) + (string-append "--libdir=" lib) + (string-append "--includedir=" include) + (string-append "--with-bz2=" + #$(this-package-input "bzip2")) + (string-append "--with-z=" + #$(this-package-input "zlib")) + (string-append "--with-pcre=" + #$(this-package-input "pcre")) + ;; Each library is built twice by default, once + ;; with "-static" in its name, and again + ;; without. + "--without-static" + "--with-dll"))))))) (outputs '("out" ; 21 MB "lib" ; 226 MB "include")) ; 33 MB (inputs - `(("bzip2" ,bzip2) - ("lmdb" ,lmdb) - ("zlib" ,zlib) - ("pcre" ,pcre) - ("perl" ,perl) - ("python" ,python-wrapper))) + (list bzip2 + lmdb + zlib + pcre + perl + python-wrapper)) (native-inputs (list cpio)) (home-page "https://blast.ncbi.nlm.nih.gov") |