diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 31 |
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))) |