基因结构注释软件PASA安装全纪录

PASA安装

• 
  
• 官方网址
  

https://github.com/PASApipeline/PASApipeline/wiki

登录mysql,创建用户

• create a user/password with read-only access
• create a user/password with all privileges

mysql -u root
mysql> GRANT SELECT ON *.* TO 'pasa'@'localhost' IDENTIFIED BY "123456";
mysql> GRANT ALL ON *.* TO 'pasa_admin'@'localhost' IDENTIFIED BY "123456";
mysql> FLUSH PRIVILEGES;

安装perl模块

• DBD::mysql

cpanm --mirror http://mirrors.163.com/cpan/ DBD::mysql

安装依赖工具，写入PATH

• Tom Wu GMAP cdna alignment utility.
• Jim Kent BLAT aligner
• Bill Pearson FASTA general sequence alignment utility. Note that the fasta utility is bundled with other utilities as part of the Fasta3 suite. The fasta utility (ie. named fasta3…) should be renamed (or symlinked to) ‘fasta’. This utility is required for annotation comparisons, but not needed for alignment assembly or alt-splicing analysis.

conda install -c bioconda gmap
conda install blat
conda install fasta3

安装UniVec数据库并格式化

cd /share/home/baishenglong/programs/seqclean-x86_64/
wget ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec
formatdb -t UniVec -i UniVec -p F 

修改默认配置文件

• cp pasa_conf/pasa.CONFIG.template pasa_conf/conf.txt

MYSQL_RW_USER=baishenglong
MYSQL_RW_PASSWORD=123456

# read-only username and password
MYSQL_RO_USER=pasa
MYSQL_RO_PASSWORD=123456
PASA_ADMIN_EMAIL=slbai01@foxmail.com
VECTOR_DB=/share/home/baishenglong/programs/seqclean-x86_64/UniVec 

• cp pasa_conf/pasa.alignAssembly.Template.txt pasa_conf/alignAssembly.config
• 此处MYSQLDB指定的为工作数据库，可任意指定，运行完一次后需要删除该数据库drop database pasa_db;，否则下次运行会报错。

MYSQLDB=pasa_db
validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=75
validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=95
validate_alignments_in_db.dbi:--NUM_BP_PERFECT_SPLICE_BOUNDARY=0

解决报错

• 报错内容
  Can’t connect to local MySQL server through socket ‘/tmp/mysql.sock’
• 建立mysql动态文件软链接到pasa默认目录下
  ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock

解决报错

• 报错内容
  Specified key was too long; max key length is 1000 bytes
• 参考资料
  

  https://sourceforge.net/p/pasa/mailman/message/30827159/

• 修改文件
  /share/home/baishenglong/programs/PASApipeline-pasa-v2.2.0/schema/cdna_alignment_mysqlschema
• 原内容

172 CREATE TABLE annotation_updates (
173   update_id int(11) NOT NULL auto_increment,
174   gene_id varchar(200) default NULL,
175  model_id varchar(200) default NULL,

• 修改后内容

172 CREATE TABLE annotation_updates (
173   update_id int(11) NOT NULL auto_increment,
174   gene_id varchar(200) default NULL,
175   model_id varchar(200) default NULL,

好啦，到这儿就可以跑啦~~~