Difference between revisions of "OrthoMCL"
From Crop Genomics Lab.
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SHOW VARIABLES LIKE 'tmpdir'; | SHOW VARIABLES LIKE 'tmpdir'; | ||
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If you get an error on MySQL restart, you may have AppArmor enabled: | If you get an error on MySQL restart, you may have AppArmor enabled: |
Revision as of 01:40, 29 February 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