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Move tests to cmake and moved edlib into external dependency
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| Original file line number | Diff line number | Diff line change |
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@@ -7,3 +7,4 @@ build/ | |
| .gdb_history | ||
| test/ | ||
| include | ||
| consensus* | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| ;; To use this file to build HEAD of smoothxg: | ||
| ;; | ||
| ;; guix build -f guix.scm | ||
| ;; | ||
| ;; To do a cross compilation build for ARM64 | ||
| ;; | ||
| ;; guix build -f guix.scm --target=aarch64-linux | ||
| ;; | ||
| ;; To get a development container (inside emacs shell will work) | ||
| ;; | ||
| ;; guix shell -C -D -f guix.scm -- bash --init-file <(echo "ln -s /bin/sh /bin/bash") | ||
| ;; | ||
| ;; and build | ||
| ;; | ||
| ;; find -name CMakeCache.txt|xargs rm -v | ||
| ;; cd build | ||
| ;; cmake -DCMAKE_BUILD_TYPE=Debug .. | ||
| ;; cmake --build . --verbose -- -j 14 && ctest . --verbose | ||
| ;; | ||
| ;; For the tests you may need /usr/bin/env. In a container create it with | ||
| ;; | ||
| ;; mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env | ||
| ;; | ||
|
|
||
| (use-modules | ||
| (ice-9 popen) | ||
| (ice-9 rdelim) | ||
| ((guix licenses) #:prefix license:) | ||
| (guix gexp) | ||
| (guix packages) | ||
| (guix download) | ||
| (guix git-download) | ||
| (guix build-system cmake) | ||
| (guix utils) | ||
| (gnu packages base) | ||
| (gnu packages compression) | ||
| (gnu packages bioinformatics) | ||
| (gnu packages build-tools) | ||
| (gnu packages commencement) ; gcc-toolchain | ||
| (gnu packages curl) | ||
| (gnu packages datastructures) | ||
| (gnu packages gdb) | ||
| (gnu packages gcc) | ||
| (gnu packages jemalloc) | ||
| (gnu packages libffi) | ||
| (gnu packages mpi) | ||
| (gnu packages python) | ||
| (gnu packages python-xyz) | ||
| (gnu packages pkg-config) | ||
| (gnu packages tls) | ||
| (gnu packages version-control) | ||
| ) | ||
|
|
||
| (define %source-dir (dirname (current-filename))) | ||
|
|
||
| (define %git-commit | ||
| (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ))) | ||
|
|
||
| (define-public smoothxg-git | ||
| (package | ||
| (name "smoothxg-git") | ||
| (version (git-version "0.3.3" "HEAD" %git-commit)) | ||
| (source (local-file %source-dir #:recursive? #t)) | ||
| (build-system cmake-build-system) | ||
| (inputs | ||
| `( | ||
| ("coreutils" ,coreutils) | ||
| ; ("cpp-httplib" ,cpp-httplib) later! | ||
| ("pybind11" ,pybind11) ;; see libstd++ note in remarks above | ||
| ; ("intervaltree" ,intervaltree) later! | ||
| ("jemalloc" ,jemalloc) | ||
| ("gcc" ,gcc-11) | ||
| ("gcc-lib" ,gcc-11 "lib") | ||
| ("gcc-toolchain" ,gcc-toolchain) | ||
| ("gdb" ,gdb) | ||
| ("git" ,git) ; pulls in perl which does not do RISV-V cross builds yet | ||
| ; ("lodepng" ,lodepng) later! | ||
| ("openmpi" ,openmpi) | ||
| ("python" ,python) | ||
| ("sdsl-lite" ,sdsl-lite) | ||
| ("libdivsufsort" ,libdivsufsort) | ||
| ("zlib" ,zlib) | ||
| ("zstd-lib" ,zstd "lib") | ||
| )) | ||
| (native-inputs | ||
| `(("pkg-config" ,pkg-config) | ||
| )) | ||
| (arguments | ||
| `(#:phases | ||
| (modify-phases | ||
| %standard-phases | ||
| ;; This stashes our build version in the executable | ||
| (add-after 'unpack 'set-version | ||
| (lambda _ | ||
| (mkdir-p "include") | ||
| (with-output-to-file "include/smoothxg_git_version.hpp" | ||
| (lambda () | ||
| (format #t "#define ODGI_GIT_VERSION \"~a\"~%" version))) | ||
| #t)) | ||
| ;; (delete 'check) | ||
| ) | ||
| ;; #:make-flags (list ,(string-append "CC=" (cc-for-target))))) | ||
| )) | ||
| (synopsis "odgi pangenome optimized dynamic sequence graph implementation") | ||
| (description | ||
| "odgi pangenome graph tooling provides an efficient, succinct dynamic | ||
| DNA sequence graph model, as well as a host of algorithms that allow | ||
| the use of such graphs.") | ||
| (home-page "https://github.com/vgteam/odgi") | ||
| (license license:expat))) | ||
|
|
||
| smoothxg-git |