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Merge branch 'eforge.v1.2'
Get the master branch back in sync with the latest developments.
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- +3 −0 AUTHORS
- +621 −0 COPYING
- +40 −0 database/README.txt
- +31 −0 database/blueprint.decode
- +126 −0 database/encode.decode
- +300 −0 database/erc.decode
- +196 −0 database/erc2-H3-all.decode
- +40 −0 database/erc2-H3K27me3.decode
- +40 −0 database/erc2-H3K36me3.decode
- +40 −0 database/erc2-H3K4me1.decode
- +40 −0 database/erc2-H3K4me3.decode
- +40 −0 database/erc2-H3K9me3.decode
- +40 −0 database/erc2.decode
- +112 −0 database/init_db.pl
- +346 −0 database/load_27k_array.pl
- +287 −0 database/load_450k_array.pl
- +416 −0 database/load_dataset.pl
- +270 −224 eForge/eForge.pm
- +61 −67 eForge/ePlot.pm
- +35 −53 eForge/eStats.pm
- +151 −81 eforge.pl
- +39 −27 webserver/INSTALL
- +85 −48 webserver/cgi-bin/index.pl
| @@ -0,0 +1,3 @@ | ||
| +eFORGE was developed by Charles Breeze while on secondment at the European Bioinformatics Institute as part of the EpiTrain Initial Training Network. | ||
| + | ||
| +The code, webserver and database are currently maintained by Charles Breeze and Javier Herrero. |
| @@ -0,0 +1,40 @@ | ||
| +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 .. |
| @@ -0,0 +1,31 @@ | ||
| +file lab datatype cell tissue shortcell individual acc url | ||
| +BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Sporadic_Burkitt_lymphoma Cell Line DG-75_Sporadic_Burkitt_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS/BP_DG-75_d01.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00C0J41.DNase.hotspot_v3.20141014.bed.gz | ||
| +BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Multiple_myeloma Cell Line U-266_Multiple_myeloma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS/BP_U-266_d01.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00CR241.DNase.hotspot_v3.20141014.bed.gz | ||
| +BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Mantle_cell_lymphoma Cell Line Z-138_Mantle_cell_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS/BP_Z-138_d01.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00CS041.DNase.hotspot_v3.20141014.bed.gz | ||
| +C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0010K46.DNase.hotspot_v3.20130415.bed.gz | ||
| +S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00CTZ41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_50_55_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0011I43.DNase.hotspot_v3.20130415.bed.gz | ||
| +S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00EPZ41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C001UY46.DNase.hotspot_v3.20130415.bed.gz | ||
| +S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00HRJ41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C004084E.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C004084E.DNase.hotspot_v3.20130415.bed.gz | ||
| +S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00HSH41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DHS CD14_positive_CD16_negative_classical_monocyte Cord Blood CD14_positive_CD16_negative_classical_monocyte Female NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C005PS4E.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00HTF41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS/C005VG45.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00JPF41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DHS CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS/C006NS47.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00JQD41.DNase.hotspot_v3.20141014.bed.gz | ||
| +C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_65_70_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS/C006UE47.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00JRB41.DNase.hotspot_v3.20141014.bed.gz | ||
| +S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ48.DNase.hotspot_v3.20130819.bed.gz | ||
| +S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00JS941.DNase.hotspot_v3.20141014.bed.gz | ||
| +S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ4A.DNase.hotspot_v3.20130819.bed.gz | ||
| +bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed.gz | ||
| +S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DHS Acute_myeloid_leukemia Bone Marrow Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS/S005FH41.DNase.hotspot_v3.20130819.bed.gz | ||
| +bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed.gz | ||
| +S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00BXV41.DNase.hotspot_v3.20141014.bed.gz | ||
| +S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00BYT41.DNase.hotspot_v3.20141014.bed.gz |
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