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-rw-r--r--gn/packages/bioinformatics.scm31
1 files changed, 8 insertions, 23 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5660470..c107c83 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -878,6 +878,7 @@ interest, and this app can provide values and figures for applicants to use.")
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(let ((sdsl-lite (assoc-ref inputs "sdsl-lite"))
+ (sufsort (assoc-ref inputs "sufsort"))
(bsort (assoc-ref inputs "bsort"))
(mmap_allocator (assoc-ref inputs "mmap-allocator"))
(tayweeargs (assoc-ref inputs "tayweeargs-source"))
@@ -901,8 +902,8 @@ interest, and this app can provide values and figures for applicants to use.")
(find-files "src" ".")
(list
(string-append sdsl-lite "/lib/libsdsl.a")
- (string-append sdsl-lite "/lib/libdivsufsort.a")
- (string-append sdsl-lite "/lib/libdivsufsort64.a")
+ (string-append sufsort "/lib/libdivsufsort.so")
+ (string-append sufsort "/lib/libdivsufsort64.so")
(string-append mmap_allocator "/lib/libmmap_allocator.a")
(string-append bsort "/lib/libbsort.a")))))))
(replace 'check
@@ -920,7 +921,8 @@ interest, and this app can provide values and figures for applicants to use.")
`(("bsort" ,ekg-bsort)
("mmap-allocator" ,ekg-mmap-allocator)
("openmpi" ,openmpi)
- ("sdsl-lite" ,sdsl-lite-gn)
+ ("sdsl-lite" ,sdsl-lite)
+ ("sufsort" ,libdivsufsort)
("zlib" ,zlib)))
(native-inputs
`(("prove" ,perl)
@@ -983,20 +985,6 @@ limited by the use of sorted disk-backed arrays and succinct rank/select
dictionaries to record a queryable version of the graph.")
(license license:expat)))
-(define sdsl-lite-gn
- (package
- (inherit sdsl-lite)
- (name "sdsl-lite-gn")
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'install 'install-libdivsufsort
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (install-file "lib/libdivsufsort.a" (string-append out "/lib"))
- (install-file "lib/libdivsufsort64.a" (string-append out "/lib"))
- #t))))))))
-
(define ekg-bsort
(let ((commit "c3ab0d3308424030e0a000645a26d2c10a59a124")
(revision "1"))
@@ -1089,11 +1077,7 @@ dictionaries to record a queryable version of the graph.")
(lambda* (#:key inputs #:allow-other-keys)
(let ((sdsl (assoc-ref inputs "sdsl-lite")))
(substitute* "makefile"
- (("VERSION .*") (string-append "VERSION = " ,version "\n"))
- (("`pkg-config --libs libdivsufsort`")
- (string-append sdsl "/lib/libdivsufsort.a"))
- (("`pkg-config --libs libdivsufsort64`")
- (string-append sdsl "/lib/libdivsufsort64.a"))))
+ (("VERSION .*") (string-append "VERSION = " ,version "\n"))))
#t))
(delete 'configure) ; no configure phase
(replace 'install
@@ -1111,12 +1095,13 @@ dictionaries to record a queryable version of the graph.")
(native-inputs
`(("pkg-config" ,pkg-config)
("protobuf" ,protobuf "static")
- ("sdsl-lite" ,sdsl-lite-gn)
+ ("sdsl-lite" ,sdsl-lite)
("sparsehash" ,sparsehash)
("zlib" ,zlib "static")))
(inputs
`(("boost" ,boost-static)
("jemalloc" ,jemalloc)
+ ("libdivsufsort" ,libdivsufsort)
("mummer" ,mummer)
("protobuf" ,protobuf)
("zlib" ,zlib)))