Difference between revisions of "OrthoMCL"
From Crop Genomics Lab.
Line 4: | Line 4: | ||
sudo vim /etc/mysql/conf.d/local.cnf | sudo vim /etc/mysql/conf.d/local.cnf | ||
+ | |||
Add: | Add: | ||
[mysqld] | [mysqld] | ||
+ | |||
tmpdir = /run/mysqld | tmpdir = /run/mysqld | ||
+ | |||
Then: | Then: | ||
sudo service mysql restart | sudo service mysql restart | ||
+ | |||
Last: | Last: | ||
Line 19: | Line 23: | ||
sudo vim /etc/apparmor.d/local/usr.sbin.mysqld | sudo vim /etc/apparmor.d/local/usr.sbin.mysqld | ||
+ | |||
Add: | Add: | ||
# Site-specific additions and overrides for usr.sbin.mysqld. | # Site-specific additions and overrides for usr.sbin.mysqld. | ||
# For more details, please see /etc/apparmor.d/local/README. | # For more details, please see /etc/apparmor.d/local/README. | ||
+ | |||
/run/mysqld/ r, | /run/mysqld/ r, | ||
+ | |||
/run/mysqld/** rwk, | /run/mysqld/** rwk, | ||
+ | |||
Then: | Then: | ||
Revision as of 07:36, 23 June 2016
mysql configuration
changing tmp folder
Here is an example to move the mysqld tmpdir from /tmp to /run/mysqld which already exists on Ubuntu 13.04 and is a tmpfs (memory/ram):
sudo vim /etc/mysql/conf.d/local.cnf
Add:
[mysqld]
tmpdir = /run/mysqld
Then:
sudo service mysql restart
Last:
SHOW VARIABLES LIKE 'tmpdir';
If you get an error on MySQL restart, you may have AppArmor enabled:
sudo vim /etc/apparmor.d/local/usr.sbin.mysqld
Add:
- Site-specific additions and overrides for usr.sbin.mysqld.
- For more details, please see /etc/apparmor.d/local/README.
/run/mysqld/ r,
/run/mysqld/** rwk,
Then:
sudo service apparmor reload
All vs All blast command
blastp -db goodProteins.fasta -query goodProteins.fasta -outfmt 6 -out goodProteins.fasta.allvall -num_threads 3 -evalue 1e-5 -seg yes -soft_masking true -max_target_seqs 999999999