Difference between revisions of "Design Specs: Configuration setup and 3rd party software install"
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+ | = configuration = | ||
+ | |||
in wormbase.conf | in wormbase.conf | ||
turn the timing&caching information on | turn the timing&caching information on | ||
− | + | timer = 1 | |
− | when people submit/update issues, email alters will be sent out from this | + | when people submit/update issues, email alters will be sent out from this address |
issue_email = oicr@wormbase.org | issue_email = oicr@wormbase.org | ||
Line 17: | Line 19: | ||
# subject Error Report from: %h; %F, line %l | # subject Error Report from: %h; %F, line %l | ||
</Plugin::ErrorCatcher::Email> | </Plugin::ErrorCatcher::Email> | ||
+ | |||
+ | wormbase user database configuration | ||
+ | <Model::Schema> | ||
+ | schema_class = WormBase::Schema | ||
+ | <connect_info> | ||
+ | dsn = dbi:mysql:wormbase_user:hostname=... | ||
+ | user = .. | ||
+ | password = .. | ||
+ | </connect_info> | ||
+ | </Model::Schema> | ||
+ | |||
+ | = third party software = | ||
+ | |||
+ | == CutyCapt == | ||
+ | |||
+ | this is used to provide pdf print function on the new site | ||
+ | |||
+ | http://cutycapt.sourceforge.net/ | ||
+ | |||
+ | installation | ||
+ | % sudo apt-get install subversion libqt4-webkit libqt4-dev g++ | ||
+ | % svn co https://cutycapt.svn.sourceforge.net/svnroot/cutycapt | ||
+ | % cd cutycapt/CutyCapt | ||
+ | % qmake | ||
+ | % make | ||
+ | |||
+ | configure path to the executable | ||
+ | <pre> | ||
+ | <Model::WormBaseAPI> | ||
+ | ... | ||
+ | |||
+ | <print> | ||
+ | PRO_EXEC = ./CutyCapt | ||
+ | </print> | ||
+ | ... | ||
+ | </Model::WormBaseAPI> | ||
+ | </pre> | ||
+ | |||
+ | == Blast/Blat == | ||
+ | |||
+ | configuration | ||
+ | <pre> | ||
+ | <blast_blat> | ||
+ | base = /usr/local/wormbase/databases/ | ||
+ | blast = /blast/ | ||
+ | SCORE_KEY_IMAGE = score_key.png | ||
+ | HSP_GENOME_LINK_PART_LIMIT = 10 | ||
+ | HSP_ALIGNMENT_IMAGE_LIMIT = 10 | ||
+ | BLAST_EXEC_DIR = /usr/local/wormbase/services/blast | ||
+ | BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient | ||
+ | b_genome = c_elegans c_briggsae ... | ||
+ | b_protein = c_elegans c_briggsae ... | ||
+ | b_gene = c_elegans ... | ||
+ | b_est = c_elegans ... | ||
+ | ARCHIVES = WS100 WS110... | ||
+ | </blast_blat> | ||
+ | </pre> | ||
+ | |||
+ | == Aligner == | ||
+ | need to installation GBrowse libraries in order for it to work! | ||
+ | |||
+ | on dev, it's under | ||
+ | /usr/local/wormbase/website/staging/extlib/gbrowse2/current/lib/perl5/x86_64-linux-gnu-thread-multi/ |
Latest revision as of 21:18, 27 January 2011
configuration
in wormbase.conf
turn the timing&caching information on
timer = 1
when people submit/update issues, email alters will be sent out from this address
issue_email = oicr@wormbase.org
email account when people register at WormBase
register_email = oicr@wormbase.org
email account for error reporting!
<Plugin::ErrorCatcher::Email> to oicr@wormbase.org from oicr@wormbase.org use_tags 1 # subject Error Report from: %h; %F, line %l </Plugin::ErrorCatcher::Email>
wormbase user database configuration
<Model::Schema> schema_class = WormBase::Schema <connect_info> dsn = dbi:mysql:wormbase_user:hostname=... user = .. password = .. </connect_info> </Model::Schema>
third party software
CutyCapt
this is used to provide pdf print function on the new site
http://cutycapt.sourceforge.net/
installation
% sudo apt-get install subversion libqt4-webkit libqt4-dev g++ % svn co https://cutycapt.svn.sourceforge.net/svnroot/cutycapt % cd cutycapt/CutyCapt % qmake % make
configure path to the executable
<Model::WormBaseAPI> ... <print> PRO_EXEC = ./CutyCapt </print> ... </Model::WormBaseAPI>
Blast/Blat
configuration
<blast_blat> base = /usr/local/wormbase/databases/ blast = /blast/ SCORE_KEY_IMAGE = score_key.png HSP_GENOME_LINK_PART_LIMIT = 10 HSP_ALIGNMENT_IMAGE_LIMIT = 10 BLAST_EXEC_DIR = /usr/local/wormbase/services/blast BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient b_genome = c_elegans c_briggsae ... b_protein = c_elegans c_briggsae ... b_gene = c_elegans ... b_est = c_elegans ... ARCHIVES = WS100 WS110... </blast_blat>
Aligner
need to installation GBrowse libraries in order for it to work!
on dev, it's under
/usr/local/wormbase/website/staging/extlib/gbrowse2/current/lib/perl5/x86_64-linux-gnu-thread-multi/