PASA安裝

• 官方網址
  

登入mysql,建立使用者

• 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;

安裝perl模組

• DBD::mysql

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

安裝依賴工具，寫入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

安裝UniVec資料庫並格式化

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

修改預設配置檔案

• 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[email protected]
VECTOR_DB=/share/home/baishenglong/programs/seqclean-x86_64/UniVec 

• cp pasa_conf/pasa.alignAssembly.Template.txt pasa_conf/alignAssembly.config
• 此處MYSQLDB指定的為工作資料庫，可任意指定，執行完一次後需要刪除該資料庫drop database pasa_db;，否則下次執行會報錯。

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

解決報錯

• 報錯內容
  Can’t connect to local MySQL server through socket ‘/tmp/mysql.sock’
• 建立mysql動態檔案軟連結到pasa預設目錄下
  ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock

解決報錯

• 報錯內容
  Specified key was too long; max key length is 1000 bytes
• 修改檔案
  /share/home/baishenglong/programs/PASApipeline-pasa-v2.2.0/schema/cdna_alignment_mysqlschema
• 原內容

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,

• 修改後內容

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，到這兒就可以跑啦~~~