Commit 00a6149a authored by PRUVOST Florent's avatar PRUVOST Florent
Browse files

add disseq (inrae/biogeco) package

parent 157135b2
......@@ -30,17 +30,17 @@
(define-public chameleon+cuda
(package
(inherit chameleon)
(name "chameleon-cuda")
(arguments
(substitute-keyword-arguments (package-arguments chameleon)
((#:configure-flags flags '())
`(cons "-DCHAMELEON_USE_CUDA=ON" ,flags))))
(inputs
`(("cuda" ,cuda)
,@(package-inputs chameleon)))
(propagated-inputs `(("starpu" ,starpu+cuda)
,@(delete `("starpu" ,starpu) (package-inputs chameleon))))))
(inherit chameleon)
(name "chameleon-cuda")
(arguments
(substitute-keyword-arguments (package-arguments chameleon)
((#:configure-flags flags '())
`(cons "-DCHAMELEON_USE_CUDA=ON" ,flags))))
(inputs
`(("cuda" ,cuda)
,@(package-inputs chameleon)))
(propagated-inputs `(("starpu" ,starpu+cuda)
,@(delete `("starpu" ,starpu) (package-inputs chameleon))))))
(define-public chameleon+mkl+mt
(package
......@@ -48,24 +48,24 @@
(name "chameleon-mkl-mt")
(arguments
(substitute-keyword-arguments (package-arguments chameleon)
((#:configure-flags flags '())
`(cons "-DBLA_VENDOR=Intel10_64lp" (cons "-DCBLAS_MT=ON" (cons "-DLAPACKE_MT=ON" ,flags))))))
((#:configure-flags flags '())
`(cons "-DBLA_VENDOR=Intel10_64lp" (cons "-DCBLAS_MT=ON" (cons "-DLAPACKE_MT=ON" ,flags))))))
(inputs `(("lapack" ,mkl)
,@(delete `("lapack" ,openblas) (package-inputs chameleon))))))
,@(delete `("lapack" ,openblas) (package-inputs chameleon))))))
(define-public chameleon+cuda+mkl+mt
(package
(inherit chameleon+mkl+mt)
(name "chameleon-cuda-mkl-mt")
(arguments
(substitute-keyword-arguments (package-arguments chameleon+mkl+mt)
((#:configure-flags flags '())
`(cons "-DCHAMELEON_USE_CUDA=ON" ,flags))))
(inputs
`(("cuda" ,cuda)
,@(package-inputs chameleon+mkl+mt)))
(propagated-inputs `(("starpu" ,starpu+cuda)
,@(delete `("starpu" ,starpu) (package-inputs chameleon+mkl+mt))))))
(inherit chameleon+mkl+mt)
(name "chameleon-cuda-mkl-mt")
(arguments
(substitute-keyword-arguments (package-arguments chameleon+mkl+mt)
((#:configure-flags flags '())
`(cons "-DCHAMELEON_USE_CUDA=ON" ,flags))))
(inputs
`(("cuda" ,cuda)
,@(package-inputs chameleon+mkl+mt)))
(propagated-inputs `(("starpu" ,starpu+cuda)
,@(delete `("starpu" ,starpu) (package-inputs chameleon+mkl+mt))))))
(define-public pastix+cuda
(package
......@@ -73,8 +73,8 @@
(name "pastix-cuda")
(arguments
(substitute-keyword-arguments (package-arguments pastix)
((#:configure-flags flags '())
`(cons "-DPASTIX_WITH_CUDA=ON" ,flags))))
((#:configure-flags flags '())
`(cons "-DPASTIX_WITH_CUDA=ON" ,flags))))
(inputs
`(("cuda" ,cuda)
("starpu" ,starpu+cuda)
......@@ -82,31 +82,31 @@
(define-public fmr
(package
(name "fmr")
(version "0")
(home-page "https://gitlab.inria.fr/compose/oldstack/fmr")
(source (git-checkout (url "git@gitlab.inria.fr:compose/oldstack/fmr.git")
(recursive? #t)))
(build-system cmake-build-system)
(arguments
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DFMR_BUILD_TESTS=ON"
"-DFMR_USE_HDF5=ON")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" , zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-1.10)
("lapack" ,mkl)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)))
(synopsis "Fast and accurate Methods for Randomized numerical linear algebra")
(description
"This project provides routines for performing low-rank matrix
(name "fmr")
(version "0")
(home-page "https://gitlab.inria.fr/compose/oldstack/fmr")
(source (git-checkout (url "git@gitlab.inria.fr:compose/oldstack/fmr.git")
(recursive? #t)))
(build-system cmake-build-system)
(arguments
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DFMR_BUILD_TESTS=ON"
"-DFMR_USE_HDF5=ON")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" , zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-1.10)
("lapack" ,mkl)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)))
(synopsis "Fast and accurate Methods for Randomized numerical linear algebra")
(description
"This project provides routines for performing low-rank matrix
approximations based on randomized techniques.")
(license license:cecill-c)))
(license license:cecill-c)))
;; FIXME: hdf5 delete in package inputs do not work
;;(define-public fmr+mpi
......@@ -123,64 +123,64 @@ approximations based on randomized techniques.")
(define-public fmr+mpi
(package
(name "fmr-mpi")
(version "0")
(home-page "https://gitlab.inria.fr/compose/oldstack/fmr")
(source (git-checkout (url "git@gitlab.inria.fr:compose/oldstack/fmr.git")
(recursive? #t)))
(build-system cmake-build-system)
(arguments
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DFMR_BUILD_TESTS=ON"
"-DFMR_USE_HDF5=ON"
"-DFMR_USE_CHAMELEON=ON")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" , zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-parallel-openmpi)
("lapack" ,mkl)
("chameleon" ,chameleon+mkl+mt)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)
("ssh" ,openssh)))
(synopsis "Fast and accurate Methods for Randomized numerical linear algebra")
(description
"This project provides routines for performing low-rank matrix
(name "fmr-mpi")
(version "0")
(home-page "https://gitlab.inria.fr/compose/oldstack/fmr")
(source (git-checkout (url "git@gitlab.inria.fr:compose/oldstack/fmr.git")
(recursive? #t)))
(build-system cmake-build-system)
(arguments
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DFMR_BUILD_TESTS=ON"
"-DFMR_USE_HDF5=ON"
"-DFMR_USE_CHAMELEON=ON")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" , zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-parallel-openmpi)
("lapack" ,mkl)
("chameleon" ,chameleon+mkl+mt)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)
("ssh" ,openssh)))
(synopsis "Fast and accurate Methods for Randomized numerical linear algebra")
(description
"This project provides routines for performing low-rank matrix
approximations based on randomized techniques.")
(license license:cecill-c)))
(license license:cecill-c)))
(define-public cppdiodon
(package
(name "cppdiodon")
(version "0")
(home-page "https://gitlab.inria.fr/diodon/cppdiodon")
(source (git-checkout (url "git@gitlab.inria.fr:diodon/cppdiodon.git")
(branch "master"))) ;or (commit "1234abc")
(build-system cmake-build-system)
(arguments
'(#:configure-flags `("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DDIODON_USE_INTERNAL_FMR=OFF")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" ,zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-1.10)
("lapack" ,mkl)
("fmr" ,fmr)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)))
(synopsis "Librairies for Multivariate Data Analysis and
(name "cppdiodon")
(version "0")
(home-page "https://gitlab.inria.fr/diodon/cppdiodon")
(source (git-checkout (url "git@gitlab.inria.fr:diodon/cppdiodon.git")
(branch "master"))) ;or (commit "1234abc")
(build-system cmake-build-system)
(arguments
'(#:configure-flags `("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DDIODON_USE_INTERNAL_FMR=OFF")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" ,zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-1.10)
("lapack" ,mkl)
("fmr" ,fmr)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)))
(synopsis "Librairies for Multivariate Data Analysis and
Dimensionality Reduction for very large datasets")
(description
"Librairies for Multivariate Data Analysis and Dimensionality
(description
"Librairies for Multivariate Data Analysis and Dimensionality
Reduction for very large datasets.")
(license license:cecill-c)))
(license license:cecill-c)))
;; FIXME: fmr and hdf5 delete in package inputs do not work
;; (define-public cppdiodon+mpi
......@@ -199,33 +199,62 @@ Reduction for very large datasets.")
(define-public cppdiodon+mpi
(package
(name "cppdiodon-mpi")
(version "0")
(home-page "https://gitlab.inria.fr/diodon/cppdiodon")
(source (git-checkout (url "git@gitlab.inria.fr:diodon/cppdiodon.git")
(branch "master"))) ;or (commit "1234abc")
(build-system cmake-build-system)
(arguments
'(#:configure-flags `("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DDIODON_USE_INTERNAL_FMR=OFF"
"-DDIODON_USE_CHAMELEON=ON")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" ,zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-parallel-openmpi)
("lapack" ,mkl)
("chameleon" ,chameleon+mkl+mt)
("fmr" ,fmr+mpi)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)
("ssh" ,openssh)))
(synopsis "Librairies for Multivariate Data Analysis and
(name "cppdiodon-mpi")
(version "0")
(home-page "https://gitlab.inria.fr/diodon/cppdiodon")
(source (git-checkout (url "git@gitlab.inria.fr:diodon/cppdiodon.git")
(branch "master"))) ;or (commit "1234abc")
(build-system cmake-build-system)
(arguments
'(#:configure-flags `("-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DDIODON_USE_INTERNAL_FMR=OFF"
"-DDIODON_USE_CHAMELEON=ON")
;; FIXME: trouble with STARPU /tmp dir.
#:tests? #f))
(inputs `(("zlib" ,zlib)
("bzip2" , bzip2)
("hdf5" , hdf5-parallel-openmpi)
("lapack" ,mkl)
("chameleon" ,chameleon+mkl+mt)
("fmr" ,fmr+mpi)))
(native-inputs `(("pkg-config" ,pkg-config)
("gfortran" ,gfortran)
("ssh" ,openssh)))
(synopsis "Librairies for Multivariate Data Analysis and
Dimensionality Reduction for very large datasets")
(description
"Librairies for Multivariate Data Analysis and Dimensionality
(description
"Librairies for Multivariate Data Analysis and Dimensionality
Reduction for very large datasets.")
(license license:cecill-c)))
(license license:cecill-c)))
(define-public disseq
(package
(name "disseq")
(version "0")
(home-page "https://gitlab.inria.fr/metabarcoding/pairwise_dis")
(source (git-checkout (url "git@gitlab.inria.fr:metabarcoding/pairwise_dis.git")
(branch "master")))
(build-system cmake-build-system)
(arguments
'(#:configure-flags `("-DBUILD_SHARED_LIBS=OFF"
"-DCMAKE_NO_SYSTEM_FROM_IMPORTED=ON"
"-DDISSEQ=ON"
"-DMPI_DISSEQ=ON")
#:phases (modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "src"))))
#:tests? #f))
(inputs `(("mpi" ,openmpi)))
(synopsis "Compute pairwise distances between reads as edit distances")
(description
"This package has been developed for computing exact distances,
without heuristics, between all pairs of reads of a NGS
sample. This is a first step for supervised or unsupervised clustering
of reads in an environmetal sample.")
(license license:cecill-c)))
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