Difference between revisions of "OrthoMCL"

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All vs All blast command
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== mysql configuration==
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=== changing tmp folder ===
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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):
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sudo vim /etc/mysql/conf.d/local.cnf
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Add:
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[mysqld]
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tmpdir = /run/mysqld
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Then:
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sudo service mysql restart
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Last:
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SHOW VARIABLES LIKE 'tmpdir';
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==================================================================
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If you get an error on MySQL restart, you may have AppArmor enabled:
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sudo vim /etc/apparmor.d/local/usr.sbin.mysqld
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Add:
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# Site-specific additions and overrides for usr.sbin.mysqld.
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# For more details, please see /etc/apparmor.d/local/README.
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/run/mysqld/ r,
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/run/mysqld/** rwk,
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Then:
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sudo service apparmor reload
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===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:

  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