diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 1 | ||||
| -rw-r--r-- | gn/packages/cwl.scm | 112 | ||||
| -rw-r--r-- | gn/packages/fpga.scm | 17 | ||||
| -rw-r--r-- | gn/packages/quality-control.scm | 172 | ||||
| -rw-r--r-- | gn/packages/riscv.scm | 81 | ||||
| -rw-r--r-- | gn/packages/virtualization.scm | 164 |
6 files changed, 0 insertions, 547 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 7c88afa..0b6521e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -23,7 +23,6 @@ #:use-module (gnu packages) #:use-module (gn packages crates-io) #:use-module (gn packages datastructures) - #:use-module (gn packages java) #:use-module (gn packages maths) #:use-module (gn packages ocaml) #:use-module (gn packages python) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm deleted file mode 100644 index fe5fcb2..0000000 --- a/gn/packages/cwl.scm +++ /dev/null @@ -1,112 +0,0 @@ -(define-module (gn packages cwl) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix download) - #:use-module (guix gexp) - #:use-module (guix packages) - #:use-module (guix build-system pyproject) - #:use-module (guix build-system python) - #:use-module (gnu packages) - #:use-module (gnu packages bioinformatics) - #:use-module (gnu packages docker) - #:use-module (gnu packages node) - #:use-module (gnu packages python-web) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages serialization) - #:use-module (gnu packages time) - #:use-module (gn packages python)) - - -(define-public cwl-runner - (package - (name "cwl-runner") - (version "1.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "cwl_runner" version)) - (sha256 - (base32 - "0011am2xqwchysdznayrmwhg4bfjl4wlq6m4k20z1m7gccyzjgw0")))) - (build-system python-build-system) - (propagated-inputs - `(("cwltool" ,cwltool))) - (home-page - "https://github.com/common-workflow-language/common-workflow-language") - (synopsis "Common workflow language reference implementation") - (description - "Common workflow language alternate entry point to allow cwl-runner -script as an implementation-agnostic script interpreter.") - (license license:asl2.0))) - -;; python-toil tightly integrates with cwltool using it as a library. So, -;; create a library version of cwltool where inputs become propagated inputs. -(define-public python-cwltool - (package - (inherit cwltool) - (name "python-cwltool") - (inputs - (list node)) - (propagated-inputs - (modify-inputs (package-inputs cwltool) - (delete "node"))))) - -(define-public python-toil - (package - (name "python-toil") - (version "6.1.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "toil" version)) - (sha256 - (base32 - "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'disable-optional-features - (lambda _ - (substitute* "requirements-cwl.txt" - ;; Loosen version restrictions on ruamel.yaml. - (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") - ;; Remove optional dependency on galaxy-util and - ;; galaxy-tool-util. TODO: Package these and restore these - ;; dependencies. - (("galaxy-util[^\n]*") "") - (("galaxy-tool-util[^\n]*") "")) - ;; Disable optional wdl, wes and mesos features. We don't yet - ;; have dependencies packaged for them. TODO: Package these - ;; dependencies and enable these features. - (substitute* "setup.py" - (("\"wdl\",") "") - (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") - "toil-cwl-runner = toil.cwl.cwltoil:main") - (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") - (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") - (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) - (propagated-inputs - (list python-addict - python-cachecontrol - python-configargparse - python-cwltool - python-dateutil - python-dill - python-docker - python-enlighten - python-psutil - python-pypubsub - python-pytz - python-pyyaml - python-requests - python-ruamel.yaml - python-typing-extensions-4.10 - python-urllib3)) - (home-page "https://github.com/DataBiosphere/toil") - (synopsis "Scalable, efficient and cross-platform workflow engine") - (description "Toil is a scalable, efficient, cross-platform pipeline -management system, written entirely in Python, and designed around the -principles of functional programming.") - (license (list license:asl2.0 ;; main license - license:expat)))) ;; src/toil/batchSystems/lsf.py and - ;; src/toil/batchSystems/lsfHelper.py diff --git a/gn/packages/fpga.scm b/gn/packages/fpga.scm deleted file mode 100644 index b8c3537..0000000 --- a/gn/packages/fpga.scm +++ /dev/null @@ -1,17 +0,0 @@ -(define-module (gn packages fpga) - #:use-module (gnu packages electronics) - #:use-module (guix git-download) - #:use-module (guix packages)) - -(define-public verilator-4.110 - (package - (inherit verilator) - (version "4.110") - (source (origin - (method git-fetch) - (uri (git-reference - (inherit (origin-uri (package-source verilator))) - (commit (string-append "v" version)))) - (sha256 - (base32 - "1lm2nyn7wzxj5y0ffwazhb4ygnmqf4d61sl937vmnmrpvdihsrrq")))))) diff --git a/gn/packages/quality-control.scm b/gn/packages/quality-control.scm deleted file mode 100644 index 692f08b..0000000 --- a/gn/packages/quality-control.scm +++ /dev/null @@ -1,172 +0,0 @@ -(define-module (gn packages quality-control) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) - #:use-module (guix utils) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system gnu) - #:use-module (guix build-system asdf) - #:use-module (gnu packages lisp-check) - #:use-module (gnu packages lisp-xyz) - #:use-module (gnu packages) - #:use-module (gnu packages check) - #:use-module (gnu packages databases) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages python-web) - #:use-module (guix build-system python) - #:use-module (gnu packages python-check)) - -(define-public libcsv - (let ((commit "b1d5212831842ee5869d99bc208a21837e4037d5") - (revision "0")) - (package - (name "libcsv") - (version commit) - (source - (origin - (method git-fetch) - (uri - (git-reference - (url "https://github.com/rgamble/libcsv") - (commit commit))) - (file-name (git-file-name name commit)) - (sha256 - (base32 "0nni9y0prz8lh3dywbha52yfg8qcf3dn0nb7iinfwlrmmamfyzg2")))) - (build-system gnu-build-system) - (arguments - `(#:make-flags - (list (string-append "CC=" ,(cc-for-target))))) - (home-page "https://github.com/rgamble/libcsv") - (synopsis "CSV library written in pure ANSI C") - (description -"CSV library written in pure ANSI C that can read and write CSV data.") - (license license:lgpl2.1+)))) - -(define-public sbcl-qc - (let ((commit "a0d8c807fa3f817f977a64f02f5f8936044050ad") - (revision "4")) - (package - (name "sbcl-qc") - (version (git-version "20220331" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.genenetwork.org/jgart/qc") - (commit commit))) - (sha256 - (base32 "12i9s1ipqarvq6gsjqycfm8d3ym7dv7vn3nxb5c6214xrd4mmzjj")) - (file-name (git-file-name name commit)))) - (build-system asdf-build-system/sbcl) - (arguments - `(#:tests? #f)) ; Need to fix tests. - (native-inputs - (list sbcl-1am)) - (inputs - (list sbcl-alexandria - sbcl-split-sequence)) - (home-page "https://git.genenetwork.org/jgart/qc/") - (synopsis "Quality control of delimited files") - (description -"@code{cl-qc} is a Common Lisp library for linting the following in -delimited text files: -@itemize -@item Whitespace -@item Floating-point number well-formedness -@item GeneChip Platform ID checks for Affymetrix, Illumina, and others -@end itemize\n") - (license license:unlicense)))) - -(define-public cl-qc - (sbcl-package->cl-source-package sbcl-qc)) - -;; The file -;; #P"/tmp/guix-build-sbcl-qc-uploads-20220301-0.76f870e.drv-0/source/strains.csv" -;; does not exist: -;; No such file or directory -#;(define-public sbcl-qc-uploads - (let ((commit "76f870efad964bf680bf633e272094082008e69c") - (revision "0")) - (package - (name "sbcl-qc-uploads") - (version (git-version "20220301" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.genenetwork.org/jgart/qc-uploads") - (commit commit))) - (sha256 - (base32 "1nzcdqjwh1xpr92d01fvlmdysxizyklaid10zrxbi12jmdydapil")) - (file-name (git-file-name name commit)))) - (build-system asdf-build-system/sbcl) - ;; needs install-file for strains.tsv. This require more testing. - ;; todo: see for an example: https://github.com/interactive-ssr/issr-server/blob/master/guix.scm#L46 - (arguments - `(#:tests? #f ; There are no tests yet. - #:asd-files '("qc-uploads.asd"))) - (inputs - (list sbcl-alexandria - sbcl-ningle - sbcl-clack - sbcl-cl-css - sbcl-cl-who - sbcl-cl-fad - sbcl-qc ; packaged in guix-bioinformatics - sbcl-woo)) - (home-page "https://git.genenetwork.org/jgart/qc-uploads/") - (synopsis "Web UI for qc") - (description -"@code{qc-uploads} provides a web UI for @code{qc}.") - (license license:expat)))) - -#;(define-public cl-qc-uploads - (sbcl-package->cl-source-package sbcl-qc-uploads)) - -#;(define-public ecl-qc-uploads - (sbcl-package->ecl-package sbcl-qc-uploads)) - -(define-public genenetwork-qc - (let ((commit "b735cae93ac8243bc9b07a10549a68330934d9bf") - (revision "2")) - (package - (name "genenetwork-qc") - (version (git-version "0.0.1" revision commit)) - (source - (origin - (method git-fetch) - (uri - (git-reference - ;;(url "https://git.genenetwork.org/fredmanglis/gnqc_py.git") - (url "https://gitlab.com/fredmanglis/gnqc_py.git") - (commit commit))) - (sha256 - (base32 "0my3zm7kc5ijsp7lmh5qf6z198x1gw1cr17230d20za65pssri3j")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; Tests requiring redis server fail. Figure out how to start redis - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest"))))))) - (inputs - (list python-mypy - python-pylint - python-pytest - python-hypothesis)) - (propagated-inputs - (list redis - mariadb - gunicorn - python-redis - python-flask - python-jsonpickle - python-mysqlclient)) - (synopsis "GeneNetwork Quality Control Application") - (description - "GeneNetwork qc is a quality control application for the data files that - eventually are used to add to the data in the GeneNetwork project.") - (home-page "https://git.genenetwork.org/fredmanglis/gnqc_py") - (license license:agpl3+)))) diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm deleted file mode 100644 index 61fc882..0000000 --- a/gn/packages/riscv.scm +++ /dev/null @@ -1,81 +0,0 @@ -;;; -;;; Commentary: -;;; -;;; This module is a temporary staging ground for Guix packages ported -;;; to RISC-V. They should be contributed upstream at the earliest. -;;; - -;;; -;;; Code: -;;; - -(define-module (gn packages riscv) - #:use-module (gn packages fpga) - #:use-module (gnu packages cpp) - #:use-module (gnu packages virtualization) - #:use-module (guix build-system gnu) - #:use-module (guix gexp) - #:use-module (guix git-download) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages)) - -;; Improvements to riscv support have been merged since the last release. -(define-public cva6 - (let ((commit "b40bb3264bc0ca0b5b9e9a3eb351cbaaa9b50b62") - (revision "1")) - (package - (name "cva6") - (version (git-version "4.2.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/openhwgroup/cva6") - (commit commit) - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "16zyfqfycii25sirh3bm80dws2fn10a02ny8kzijr0p0a1azklmv")))) - (build-system gnu-build-system) - (arguments - (list - #:tests? #f - #:make-flags #~(list "verilate" - ;; Dummy RISCV to suppress Makefile error. - "RISCV=foo") - #:phases - #~(modify-phases %standard-phases - ;; Patch cva6 to print to stdout correctly. See - ;; https://github.com/openhwgroup/cva6/issues/748 - (add-after 'unpack 'fix-stdout - (lambda _ - (substitute* "corev_apu/tb/rvfi_tracer.sv" - (("rvfi_i\\[i\\].insn == 32'h00000073") - "0")))) - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) - (copy-file "work-ver/Variane_testharness" - (string-append bin "/ariane")))))))) - (inputs - (list spike verilator-4.110)) - (home-page "https://docs.openhwgroup.org/projects/cva6-user-manual/") - (synopsis "Application class 6-stage RISC-V CPU") - (description "CVA6 is a 6-stage, single issue, in-order CPU which -implements the 64-bit RISC-V instruction set. It fully implements I, -M, A and C extensions as specified in Volume I: User-Level ISA V 2.3 -as well as the draft privilege extension 1.10. It implements three -privilege levels M, S, U to fully support a Unix-like operating -system. Furthermore it is compliant to the draft external debug spec -0.13. - -It has configurable size, separate TLBs, a hardware PTW and -branch-prediction (branch target buffer and branch history table). The -primary design goal was on reducing critical path length.") - (license (list license:asl2.0 - license:bsd-3 - ;; TODO: Add Solderpad Hardware license. - ))))) diff --git a/gn/packages/virtualization.scm b/gn/packages/virtualization.scm deleted file mode 100644 index b176ec7..0000000 --- a/gn/packages/virtualization.scm +++ /dev/null @@ -1,164 +0,0 @@ -(define-module (gn packages virtualization) - #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix gexp) - #:use-module (guix utils) - #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system scons) - #:use-module (gnu packages) - #:use-module (gnu packages boost) - #:use-module (gnu packages compression) - #:use-module (gnu packages cpp) - #:use-module (gnu packages graphviz) - #:use-module (gnu packages image) - #:use-module (gnu packages m4) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages protobuf) - #:use-module (gnu packages python) - #:use-module (gnu packages python-build) - #:use-module (gnu packages python-xyz) - #:use-module (past packages python27)) - -(define-public gem5 - (package - (name "gem5") - (version "22.1.0.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gem5.googlesource.com/public/gem5") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1kcdn8rawzhf88lcb2app8m1r1px4ba041kyl7xigslix7qs05k3")) - (snippet - #~(begin - (use-modules (guix build utils)) - ;; For reproducibility. - (substitute* "src/base/date.cc" - (("__DATE__") "\"1970-01-01\"") - (("__TIME__") "\"00:00:00\"")) - ;; Remove vendored pybind11. - (substitute* "ext/sst/Makefile" - (("-I../../ext/pybind11/include/") - "${shell pybind11-config --includes}")) - (substitute* "SConstruct" - ((".*pybind11.*") "")) - (delete-file-recursively "ext/pybind11"))))) - (build-system scons-build-system) - (arguments - `(#:scons-flags - (list "--verbose") - #:build-targets '("build/ARM/gem5.opt" - "build/MIPS/gem5.opt" - "build/NULL/gem5.opt" - "build/POWER/gem5.opt" - "build/RISCV/gem5.opt" - "build/SPARC/gem5.opt" - "build/X86/gem5.opt") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "SConstruct" - ;; Scons does not use the environment variables by default, - ;; but this substitution makes it do so. - ;(("main = Environment") - ; "main = Environment(ENV=os.environ)\nmain = Environment") - ;; Force adding missing includes into the environment. - (("main\\.Append\\(CPPPATH=\\[Dir\\('" all) - (string-append - all (assoc-ref inputs "kernel-headers") "/include')])\n" - all (assoc-ref inputs "libpng") "/include')])\n" - all (assoc-ref inputs "pybind11") "/include')])\n" - all (assoc-ref inputs "zlib") "/include')])\n" - all))) - (substitute* "ext/libelf/SConscript" - (("m4env\\.Tool" all) - (string-append - "m4env.Append(CPPPATH=[Dir('" - (assoc-ref inputs "kernel-headers") - "/include')])\n" - all))) - (substitute* "ext/libelf/native-elf-format" - (("cc") ,(cc-for-target))))) - ;; This uses the cached results from the previous 'build phase. - ;; Move to after 'install and delete build dir first? - (replace 'check - (lambda* (#:key tests? #:allow-other-keys #:rest args) - (when tests? - (apply (assoc-ref %standard-phases 'build) - #:build-targets '("build/NULL/unittests.opt") - args)))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin/"))) - (mkdir-p bin) - (for-each - (lambda (arch) - (when (directory-exists? - (string-append "build/" (string-upcase arch))) - (copy-file - (string-append "build/" (string-upcase arch) "/gem5.opt") - (string-append bin "gem5-" arch ".opt")) - (copy-file - (string-append "build/" (string-upcase arch) "/gem5py") - (string-append bin "gem5py-" arch)) - (copy-file - (string-append "build/" (string-upcase arch) "/gem5py_m5") - (string-append bin "gem5py_m5-" arch)))) - (list "arm" "mips" "null" "power" "riscv" "sparc" "x86"))))) - (add-after 'install 'install-configs - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (dest (string-append out "/share/gem5/configs"))) - (copy-recursively "configs" dest)))) - (add-after 'install 'wrap-binaries - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each - (lambda (file) - (wrap-program file - `("GUIX_PYTHONPATH" ":" prefix - (,(getenv "GUIX_PYTHONPATH"))))) - (find-files (string-append out "/bin"))))))))) - (inputs - (list gperftools - libpng - protobuf - pybind11 - python - python-pydot - python-six - zlib)) - (native-inputs - (list boost - m4 - pkg-config)) - (home-page "http://gem5.org/") - (synopsis "Modular platform for computer-system architecture research") - (description "The gem5 simulator is a modular platform for computer-system -architecture research, encompassing system-level architecture as well as -processor microarchitecture.") - (license license:bsd-2))) - -(define-public gem5-riscv - (package - (inherit gem5) - (name "gem5-riscv") - (arguments - (substitute-keyword-arguments (package-arguments gem5) - ((#:build-targets _ '()) - `(list "build/RISCV/gem5.opt")) - ((#:phases phases) - `(modify-phases ,phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (install-file "build/RISCV/gem5.opt" bin) - (install-file "build/RISCV/gem5py" bin) - (install-file "build/RISCV/gem5py_m5" bin)))))))))) |