me
/
guix
Archived
1
0
Fork 0
Code

Revert "gnu: blast+: Update to 2.6.0." 

This reverts commit 18dea67dc3.
master
Leo Famulari 2017-07-06 19:38:52 -04:00
parent 5dfbd76971
commit 0a66c38764
No known key found for this signature in database
GPG Key ID: 2646FA30BACA7F08
1 changed files with 9 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

25
gnu/packages/bioinformatics.scm
View File

@ -956,7 +956,7 @@ package provides command line tools using the Bio++ library.")
(define-public blast+ (define-public blast+
(package (package
(name "blast+") (name "blast+")
(version "2.6.0") (version "2.4.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -964,15 +964,13 @@ package provides command line tools using the Bio++ library.")
version "/ncbi-blast-" version "+-src.tar.gz")) version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256 (sha256
(base32 (base32
"15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
(patches (search-patches "blast+-fix-makefile.patch"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
;; Remove bundled bzip2, zlib and pcre. ;; Remove bundled bzip2 and zlib
(delete-file-recursively "c++/src/util/compress/bzip2") (delete-file-recursively "c++/src/util/compress/bzip2")
(delete-file-recursively "c++/src/util/compress/zlib") (delete-file-recursively "c++/src/util/compress/zlib")
(delete-file-recursively "c++/src/util/regexp")
(substitute* "c++/src/util/compress/Makefile.in" (substitute* "c++/src/util/compress/Makefile.in"
(("bzip2 zlib api") "api")) (("bzip2 zlib api") "api"))
;; Remove useless msbuild directory ;; Remove useless msbuild directory
@ -981,8 +979,9 @@ package provides command line tools using the Bio++ library.")
#t)))) #t))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(;; There are two(!) tests for this massive library, and both fail with `(;; There are three(!) tests for this massive library, and all fail with
;; "unparsable timing stats". ;; "unparsable timing stats".
;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
#:tests? #f #:tests? #f
@ -1015,7 +1014,6 @@ package provides command line tools using the Bio++ library.")
;; Rewrite hardcoded paths to various tools ;; Rewrite hardcoded paths to various tools
(substitute* (append '("src/build-system/configure.ac" (substitute* (append '("src/build-system/configure.ac"
"src/build-system/configure" "src/build-system/configure"
"src/build-system/helpers/run_with_lock.c"
"scripts/common/impl/if_diff.sh" "scripts/common/impl/if_diff.sh"
"scripts/common/impl/run_with_lock.sh" "scripts/common/impl/run_with_lock.sh"
"src/build-system/Makefile.configurables.real" "src/build-system/Makefile.configurables.real"
@ -1064,22 +1062,17 @@ package provides command line tools using the Bio++ library.")
(assoc-ref inputs "bzip2")) (assoc-ref inputs "bzip2"))
(string-append "--with-z=" (string-append "--with-z="
(assoc-ref inputs "zlib")) (assoc-ref inputs "zlib"))
(string-append "--with-pcre="
(assoc-ref inputs "pcre"))
;; Each library is built twice by default, once ;; Each library is built twice by default, once
;; with "-static" in its name, and again ;; with "-static" in its name, and again
;; without. ;; without.
"--without-static" "--without-static"
"--with-dll")))))))) "--with-dll"))))))))
(outputs '("out" ; 21 MB (outputs '("out" ; 19 MB
"lib" ; 226 MB "lib" ; 203 MB
"include")) ; 33 MB "include")) ; 32 MB
(inputs (inputs
`(("bzip2" ,bzip2) `(("bzip2" ,bzip2)
("zlib" ,zlib) ("zlib" ,zlib)))
("pcre" ,pcre)
("perl" ,perl)
("python" ,python-wrapper)))
(native-inputs (native-inputs
`(("cpio" ,cpio))) `(("cpio" ,cpio)))
(home-page "http://blast.ncbi.nlm.nih.gov") (home-page "http://blast.ncbi.nlm.nih.gov")