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authorEfraim Flashner2023-09-24 13:06:48 +0300
committerEfraim Flashner2023-09-24 13:39:33 +0300
commita295df1e9e233df66e4e70b55af01909c5cc9b06 (patch)
tree1ce58cc1f9ae2944b3062808c846c012342877b7 /gn
parentd73c21e18365433b78ae5f92d80919ed8f6caa04 (diff)
downloadguix-bioinformatics-a295df1e9e233df66e4e70b55af01909c5cc9b06.tar.gz
smoothxg: Link with sdsl-lite
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm15
1 files changed, 15 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a043358..c833e6a 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1705,6 +1705,19 @@ dictionaries to record a queryable version of the graph.")
#~(list (string-append "CC = " #$(cc-for-target)))
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'link-with-some-shared-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("CMakeLists.txt"
+ "deps/mmmulti/CMakeLists.txt"
+ "deps/odgi/deps/mmmulti/CMakeLists.txt")
+ (("\".*libsdsl\\.a\"") "\"-lsdsl\"")
+ (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"")
+ (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"")
+ (("\\$\\{sdsl-lite_INCLUDE\\}")
+ (search-input-directory inputs "/include/sdsl"))
+ (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}")
+ (dirname
+ (search-input-file inputs "/include/divsufsort.h"))))))
(add-before 'build 'build-abPOA
(lambda* (#:key make-flags #:allow-other-keys)
;; This helps with portability to other architectures.
@@ -1715,9 +1728,11 @@ dictionaries to record a queryable version of the graph.")
(apply invoke "make" "libabpoa" make-flags)))))))
(inputs
(list jemalloc
+ libdivsufsort
openmpi
pybind11
python
+ sdsl-lite
zlib
(list zstd "lib")))
(native-inputs