Difference between revisions of "OrthoMCL"
From Crop Genomics Lab.
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− | All vs All blast command | + | == 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 | 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 |
Revision as of 01:39, 29 February 2016
Contents |
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