基因结构注释软件PASA安装全纪录

科技前沿 • 2025-02-13 23:38 • 阅读 60

大家好，我是讯享网，很高兴认识大家。

PASA安装

官方网址

讯享网

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 ""; mysql> GRANT ALL ON *.* TO 'pasa_admin'@'localhost' IDENTIFIED BY ""; mysql> FLUSH PRIVILEGES;

讯享网

安装perl模块

DBD::mysql

讯享网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

讯享网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= # read-only username and password MYSQL_RO_USER=pasa MYSQL_RO_PASSWORD= PASA_ADMIN_EMAIL= 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。

讯享网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//
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

讯享网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~~~

基因结构注释软件PASA安装全纪录

PASA安装

登录mysql,创建用户

安装perl模块

安装依赖工具，写入PATH

安装UniVec数据库并格式化

修改默认配置文件

解决报错

解决报错

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