blob: 884a7b9a8e3c137efa6cd907ec581ed009a1a9ee (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
(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))
(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 "ed4254445b7dc247fa27d9189fd03841ad74f568")
(revision "3"))
(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.
#:asd-files '("qc.asd")))
(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:llgpl))))
(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))
|
