blob: c54a3bbd968413f1e6fac70a0d5735770da7f952 (
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
128
|
(define-module (gn services genecup-container))
(use-modules (gnu)
(guix download)
(guix modules)
(guix packages)
(guix records)
(ice-9 match))
(use-service-modules shepherd)
(use-package-modules certs compression)
(define-record-type* <genecup-configuration>
genecup-configuration
make-genecup-configuration
genecup-configuration?
(package genecup-configuration-package ; package
(default genecup)))
(define %punkt.zip
(origin
(method url-fetch)
(uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
(sha256
(base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
(define genecup-activation
(match-lambda
(($ <genecup-configuration> package)
#~(begin
(let ((nltk_data "/var/cache/nltk_data/tokenizers")
(data_dir "/export/ratspub"))
(unless (file-exists? "/export2/PubMed")
(mkdir-p "/export2/PubMed"))
(unless (file-exists? nltk_data)
(begin
;; The correct way would be to use python-nltk to download the data
;; python3 -m nltk.downloader -d /var/cache/nltk_data punkt
(mkdir-p nltk_data)
(chdir nltk_data)
(invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip)))
(unless (file-exists? (string-append data_dir "/userspub.sqlite"))
(begin
(install-file #$(file-append package "/userspub.sqlite") data_dir)
(chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
(define genecup-shepherd-service
(match-lambda
(($ <genecup-configuration> package)
(with-imported-modules (source-module-closure
'((gnu build shepherd)
(gnu system file-systems)))
(list (shepherd-service
(provision '(genecup))
(requirement '(networking))
(modules '((gnu build shepherd)
(gnu system file-systems)))
(start #~(make-forkexec-constructor/container
(list #$(file-append package "/server.py"))
;; Needs to run from the directory it is located in.
#:directory #$package
#:log-file "/var/log/genecup.log"
;; We don't need to set TMPDIR because we're inside a container.
#:environment-variables
'("EDIRECT_PUBMED_MASTER=/export2/PubMed"
"NLTK_DATA=/var/cache/nltk_data"
"PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt")
#:mappings (list (file-system-mapping
(source "/export2/PubMed")
(target source)
(writable? #t))
(file-system-mapping
(source "/export/ratspub")
(target source)
(writable? #t))
(file-system-mapping
(source "/var/cache/nltk_data")
(target source))
(file-system-mapping
(source "/etc/ssl/certs")
(target source)))))
(stop #~(make-kill-destructor))))))))
(define genecup-service-type
(service-type
(name 'genecup)
(extensions
(list
(service-extension shepherd-root-service-type
genecup-shepherd-service)
(service-extension activation-service-type
genecup-activation)
;; Make sure we get all the dependencies of Genecup.
(service-extension profile-service-type
(compose list genecup-configuration-package))))
(default-value (genecup-configuration))
(description
"Run a GeneCup Webserver.")))
(operating-system
(host-name "genecup")
(timezone "Etc/UTC")
(locale "en_US.utf8")
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(targets '("does-not-matter"))))
(file-systems (list (file-system
(device "does-not-matter")
(mount-point "/")
(type "does-not-matter"))))
;; TODO: A more minimal kernel for use in a docker image
;; (kernel linux-libre-vm)
;; No firmware for VMs.
(firmware '())
(packages (cons nss-certs %base-packages)) ;(list nss-certs))
(services (list (service genecup-service-type
(genecup-configuration
;; genecup for docker, genecup-with-tensorflow-native for architecture specific speed optimizations.
;(package genecup))))))
(package genecup-with-tensorflow-native))))))
;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-container.scm --network --share=/export2/PubMed=/export2/PubMed --share=/export/ratspub=/export/ratspub
;; For docker it isn't necessary to list the shared folders at build time.
;; guix system docker-image -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-container.scm --network
;; Docker instructions:
;; docker load --input genecup-docker-image.tar.gz
;; docker run -d --privileged --net=host --name genecup --volume /path/to/PubMed:/export2/PubMed guix
|
