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Diffstat (limited to 'gn/packages/quality-control.scm')
| -rw-r--r-- | gn/packages/quality-control.scm | 176 |
1 files changed, 0 insertions, 176 deletions
diff --git a/gn/packages/quality-control.scm b/gn/packages/quality-control.scm deleted file mode 100644 index f0a9c2f..0000000 --- a/gn/packages/quality-control.scm +++ /dev/null @@ -1,176 +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)) - -(define-public ecl-qc - (sbcl-package->ecl-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+)))) |