blob: a0947ec92e9acc9d8a2faeaf3ff184796b232c23 (
about) (
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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
|
;; See dockerfile for some clarification about choices:
;; https://github.com/icebert/docker_ucsc_genome_browser/blob/master/Dockerfile
;; http://genome.ucsc.edu/goldenPath/help/mirrorManual.html
(define-module (gn services genome-browser))
(use-modules (gnu)
(guix build utils)
(guix packages)
(gn packages bioinformatics))
(use-service-modules
databases
networking
web)
(use-package-modules
bash
databases
ghostscript
wget)
(define %hg.conf
(mixed-text-file "hg.conf"
"browser.documentRoot=" ucsc-genome-browser "/html\n"
;"db.host=localhost\n"
;"db.user=readonly\n"
;"db.password=access\n"
"db.host=penguin2\n"
"db.user=webqtlout\n"
"db.password=webqtlout\n"
"db.trackDb=trackDb\n"
;"db.port=13306\n"
"gbdbLoc1=/gbdb/\n"
"gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/\n"
;# To disable on-the-fly loading of mysql data, comment out these lines.
"slow-db.host=genome-mysql.soe.ucsc.edu\n"
"slow-db.user=genomep\n"
"slow-db.password=password\n"
"defaultGenome=Mouse\n"
"central.db=hgcentral\n"
;"central.host=localhost\n"
;"central.socket=/run/mysqld/mysqld.sock\n" ; default for mysql service
;"central.user=readwrite\n"
;"central.password=update\n"
"central.host=penguin2\n"
"central.user=webqtlout\n"
"central.password=webqtlout\n"
"central.domain=\n"
"backupcentral.db=hgcentral\n"
"backupcentral.host=penguin2\n"
"backupcentral.user=webqtlout\n"
"backupcentral.password=webqtlout\n"
"backupcentral.domain=\n"
"freeType=on\n"
"freeTypeDir=" gs-fonts "/share/fonts/type1/ghostscript\n"
;"hgc.psxyPath=" gmt "/bin/psxy"
;"hgc.ps2rasterPath=" gmt "/bin/ps2raster"
"hgc.ghostscriptPath=" ghostscript "/bin/gs\n" ; needed?
"udc.cacheDir=/var/cache/genome/udcCache\n")) ; default is /tmp/udcCache
(define %startup-script
(mixed-text-file "create_databases.sh"
wget "/bin/wget http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql\n"
bash-minimal "/bin/sh " (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh\n"
mariadb "/bin/mysql -e \"create database hgcentral;\" mysql\n"
mariadb "/bin/mysql hgcentral < hgcentral.sql\n"
coreutils-minimal "/bin/mkdir -p /var/cache/genome\n"
coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n"))
;; This might be useful as a one-off shepherd job.
;(define %genome-activation-script
; #~(begin
; ;(unless (file-exists? "/var/lib/mysql/hgcentral")
; ; (invoke #$(file-append wget "/bin/wget") "http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql" "-O" "/var/lib/mysql/hgcentral.sql")
; ; ;(invoke "sh" #$(file-append (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh"))
; ; (invoke #$(file-append mariadb "/bin/mysql") "-e" "\"create database hgcentral;\"" "mysql")
; ; (invoke #$(file-append mariadb "/bin/mysql") "hgcentral" "<" "/var/lib/mysql/hgcentral.sql"))
; (unless (file-exists? "/var/www/html/trash")
; (mkdir-p "/var/www/html/trash"))
; (unless (file-exists? "/var/cache/genome")
; (mkdir-p "/var/cache/genome"))
; (for-each (lambda (file)
; (chown file (passwd:uid "httpd") (passwd:gid "httpd")))
; (append (find-files "/var/cache/genome" #:directories? #t)
; (find-files "/var/www/html/trash" #:directories? #t)))
; (for-each (lambda (file)
; (chown file (passwd:uid "mysql") (passwd:gid "mysql")))
; (find-files "/var/lib/mysql" #:directories? #t))))
;(define %one-month-files
; (let ((%one-month (* 60 60 24 30)))
; (find-files "/var/cache/genome" (lambda (file stat)
; (> (stat:atime stat) %one-month)))))
;; TODO:
;; create 'daily clean' mcron scripts. Only needed in /var/cache/genome grows too large.
;; use rsync to make sure mouse genome data is kept up-to-date.
(define ucsc-genome-browser-port 4322)
(operating-system
(host-name "genome-browser")
(timezone "Etc/UTC")
(locale "en_US.utf8")
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(file-systems %base-file-systems)
;; No firmware for VMs
(firmware '())
(packages (cons* mariadb ; for create-db script, interacting with database if necessary
%base-packages))
(services
(list ;(service mysql-service-type
; (mysql-configuration
; (port 13306))) ; don't overlap with penguin2's mariadb
(service special-files-service-type
`(;("/root/create_hgcentral" ,%startup-script)
("/var/lib/genome/hg.conf" ,%hg.conf)))
(service inetd-service-type
(inetd-configuration
(entries
(list
(inetd-entry
(node "127.0.0.1")
(name "blat") ; yes, it's named blat
(socket-type 'stream)
(protocol "tcp") ; probably?
(wait? #f)
(user "httpd:httpd") ; or dedicated user. Needs write access.
(program (file-append ucsc-genome-browser "/bin/gfServer"))
(arguments
'("gfServer" "dynserver" "/gbdb")))))))
(syslog-service) ; needed by inetd
(service httpd-service-type
(httpd-configuration
(config
(httpd-config-file
(document-root (file-append ucsc-genome-browser "/html"))
(server-name "Genome_Browser")
(listen (list (number->string ucsc-genome-browser-port)))
(modules
(cons*
(httpd-module
(name "cgid_module")
(file "modules/mod_cgid.so"))
(httpd-module
(name "include_module")
(file "modules/mod_include.so"))
%default-httpd-modules))
(extra-config (list "\
TypesConfig etc/httpd/mime.types
# More logs for more debugging.
LogFormat \"%h %l %u %t \\\"%r\\\" %>s %b\" common
CustomLog /var/log/httpd/combined_log common
#LogLevel debug
# cgid.sock needs to be creatable, not in the store
ScriptSock /var/run/cgid.sock
#XBitHack needs to not be inside the VirtualHost block.
XBitHack On
# same as 'listen' above
<VirtualHost *:" (number->string ucsc-genome-browser-port) ">
DocumentRoot " ucsc-genome-browser "/html
Alias /bin " ucsc-genome-browser "/bin
#Alias /cgi-bin " ucsc-genome-browser "/cgi-bin # causes cgi scripts to fail to render
Alias /favicon.ico " ucsc-genome-browser "/html/faviconRR.ico
Alias /htdocs " ucsc-genome-browser "/htdocs
#Alias /htdocs " ucsc-genome-browser "/html
Alias /var/www/html/trash /var/cache/genome
Alias /var/cache/genome /var/cache/genome
<Directory " ucsc-genome-browser "/html>
Options +Includes
#Options +Includes +FollowSymLinks +Indexes
AllowOverride None
<IfModule mod_authz_host.c>
Require all granted
SSILegacyExprParser on
</IfModule>
</Directory>
ScriptAlias /cgi-bin " ucsc-genome-browser "/cgi-bin
<Directory " ucsc-genome-browser "/cgi-bin>
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
#Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks
Order allow,deny
#SetHandler cgi-script
Require all granted
Allow from all
</Directory>
<Directory /var/cache/genome>
Options MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Directory>
# Upstream default location, possibly expected by software
<Directory /var/www/html/trash>
Options MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Directory>
</VirtualHost>")))))))))
;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genome-browser.scm --network --share=/export/efraimf/UCSC_Genome/gbdb=/gbdb --share=/export/efraimf/UCSC_Genome/var-lib-mysql=/var/lib/mysql --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/cache/genome --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/www/html/trash
;; xdg-open http://localhost:4322
|
