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Get_FTP_bed_files_pyconf.pm
Get_FTP_bed_files_pyconf.pm
 
 
README.md
README.md
 
 

README.md

An eHive pipeline for downloading ChIP-Seq peak call bed files from FTP

This is a eHive configuration file for donwloading ChIP-Seq peak call bed files from Blueprint's FTP site and load them to a MySQL database. This pipeline uses the Python3 wrapper script of the eHive codebase. It utilises an index file from the Blueprint project for collecting the file url information.

Setup Pipeline

Get python_script repo


  git clone https://github.com/avikdatta/python_scripts.git

Downlonload eHive from Git


  git clone https://github.com/Ensembl/ensembl-hive.git

Set Environment


  export PYTHONPATH=$PYTHONPATH:/path/python_scripts/lib
  export PYTHONPATH=$PYTHONPATH:/path/ensembl-hive/wrappers/python3
  export PERL5LIB=$PERL5LIB:/path/python_scripts/lib
  export PERL5LIB=$PERL5LIB:/path/ensembl-hive/modules
  export PATH=$PATH:/path/ensembl-hive/scripts

Create MySQL table for storing files


  mysql -hHOST -PPORT -uUSER -pPASS bed_files < python_scripts/scripts/load_ftp_bed_files_in_db/db_table.sql

Initialise pipeline


   init_pipeline.pl Hive::PipeConfig::Get_FTP_bed_files::Get_FTP_bed_files_pyconf \
  -user HIVE_DBUSER \
  -password HIVE_DBPASS \
  -store_dir /path/store_dir \
  -file_dbname DBNAME \
  -file_dbuser DBUSER \
  -file_dbpass DBPASS

Seed pipeline


  seed_pipeline.pl \
  -url mysql://HIVE_DBUSER:HIVE_DBPASS@DBHOST/HIVE_DBNAME \
  -logic_name 'bed_file_factory' \
  -input_id '{ "index_file"=>"/path/index_file"}'

Run pipeline


  beekeeper.pl -url mysql://HIVE_DBUSER:HIVE_DBPASS@DBHOST/HIVE_DBNAME -loop

Requirements