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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:


If you get an error on MySQL restart, you may have AppArmor enabled:

sudo vim /etc/apparmor.d/local/usr.sbin.mysqld Add:

  1. Site-specific additions and overrides for usr.sbin.mysqld.
  2. 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