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| This directory contains the scripts and files necessary to rebuild the eFORGE database from scratch. | |
| In summary, the steps are: | |
| - Create an empty DB | |
| - Load the information about the arrays | |
| - Load the dataset with DHS, Histone peaks, etc | |
| - Move the DB to its final destination | |
| 1. CREATE AN EMPTY DATABASE | |
| Please refer to the help of init_db.pl for information about the different options | |
| rm eforge_1.2.db | |
| perl init_db.pl --db_name eforge_1.2.db | |
| 2. LOAD THE ARRAYS | |
| Please refer to the help of load_450k_array.pl for information about the different options | |
| perl load_450k_array.pl --work_dir input --db_name eforge_1.2.db | |
| perl load_27k_array.pl --work_dir input --db_name eforge_1.2.db | |
| 3. LOAD THE DATASETS | |
| Please refer to the help of load_dataset.pl for information about the different options | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/ | |
| perl load_dataset.pl --db_name eforge_1.2.db --tag blueprint --name 'Blueprint - DHS' --decode_file blueprint.decode --work_dir input/blueprint/ | |
| 4. MOVE THE DATABASE TO ITS FINAL LOCATION | |
| mv eforge_1.2.db .. |