Installation FAQs
Solutions
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How do I resolve the max allowed packet error while installing cgsp database
in mysql?
If you get an error like :
ERROR 1153 (08S01) at line 798: Got a packet bigger than 'max_allowed_packet' bytes
make: *** [databases_install] Error 1
The mysql server's default max_allowed_packet value is 1MB. You can increase this size by setting it to a larger value. One of the solution is :- Go to you home directory ( [SHELL-some_working_directory]$ cd ~)
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Create a new hidden file called "
.my.cnf"
NOTE: make sure there is a (DOT) before the file name and the permissions are set as executatble.
[SHELL-home]$ emacs .my.cnf -
now type the following lines in that empty file:
[mysqld]
max_allowed_packet=32M - You can check the value of the max_allowed_packet by the query in mysql.
[SHELL]$ cd ~ [SHELL-home]$ emacs .my.cnf[mysqld] max_allowed_packet=32M[SHELL-home]$ mysql -u username -p password -h mysql-server mysql> show variables like 'max_allowed_packet%'; +--------------------+----------+ | Variable_name | Value | +--------------------+----------+ | max_allowed_packet | 33554432 | +--------------------+----------+ 1 row in set (0.00 sec)
Please see the mysql documentation for more details or click here to go the online documentation.
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How do I resolve
the Can`t locate BIO/Tools error while
editing a gene in Genome Viewer?
If you get an error like :Software error:
Can't locate Bio/Tools/CodonTable.pm in @INC (@INC contains: ../ ../shared ../../ /Library/WebServer/CGI-Executables/chado_prok_manatee/start_site_editor /Library/WebServer/CGI-Executables/chado_prok_manatee/start_site_editor/.. /Library/WebServer/CGI-Executables/chado_prok_manatee/start_site_editor/../shared /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) at /Library/WebServer/CGI-Executables/chado_prok_manatee/start_site_editor/ss_editor.cgi line 14.
BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/chado_prok_manatee/start_site_editor/ss_editor.cgi line 14.
For help, please send mail to the webmaster (you@example.com), giving this error message and the time and date of the error.
This means that bioperl module is not present on your system.
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Please install bioperl on your machine.
Click here to see the installation instructions.
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Please install bioperl on your machine.
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How do I resolve
the error fetching data! error while
changing the start site of gene in Genome Viewer
If you get an error like while editing a start site:
This means that perl module JSON is not installed on you system.
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Please install JSON perl modules on your machine.
[SHELL]$sudo perl -MCPAN -e 'install JSON'
[SHELL]$sudo perl -MCPAN -e 'install JSON::Any'
Click here to see the installation instructions.
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Please install JSON perl modules on your machine.
