pkuksa/filer repository overview

FILER provides a framework for Harmonizing and Querying Large-Scale Functional Genomics Knowledge. This docker contains all the necessary libraries/software tools for accessing and querying FILER data.

⁠Download FILER docker:

docker pull pkuksa/filer

To download specific version use, e.g.:

docker pull pkuksa/filer:v1.1

⁠Getting an interactive session inside FILER docker:

docker run --rm -it pkuksa/filer /bin/bash

By default, you will start in /opt folder

FILER scripts are pre-installed in /opt/FILER_scripts

Sample of FILER data is pre-installed in /opt/sample_FILER_data

⁠Querying/accessing FILER data

FILER docker contains a small sample of FILER data (10 tracks): /opt/sample_FILER_data

docker run --rm -it pkuksa/filer /bin/bash
cd /opt
bash FILER_scripts/data_querying/get_data_region.sh --trackID NGEN000601 --region chr1:50000-1500000 --includeMetadata 1 --outputFormat json --configFile filer.ini > out.overlaps.json
bash FILER_scripts/data_querying/get_data_region.sh --trackID NGEN000601 --region chr1:50000-1500000 --includeMetadata 1 --outputFormat bed --configFile filer.ini > out.overlaps.bed
bash FILER_scripts/data_querying/get_overlapping_tracks_by_coord.sh --region chr1:1103243-1203243 --outputDir query_out --genomeBuild hg19 --configFile filer.ini
bash FILER_scripts/data_querying/get_metadata.sh ".\"Data Source\" == \"ENCODE\" and .\"cell type\" == \"CD14+ monocyte\" " hg19 filer.ini > out.metadata.json

For further details on the syntax, usage, and example commands please refer to the README (https://bitbucket.org/wanglab-upenn/FILER⁠) and the help (--help) for individual scripts.

⁠Installing hg38/hg19 FILER data

You can also mount a host/working directory (will be accessible both outside docker and inside the docker):

docker run --rm -it -v your/working/directory/for/FILER:/mnt/data/FILER pkuksa/filer /bin/bash

This working directory can be used, for example, to install FILER data from inside docker:

/opt/FILER_scripts/install_filer.sh /mnt/data/FILER/FILER_hg38 https://tf.lisanwanglab.org/GADB/metadata/filer.latest.hg38.template /opt/filer.ini

/opt/FILER_scripts/install_filer.sh /mnt/data/FILER/FILER_hg19 https://tf.lisanwanglab.org/GADB/metadata/filer.latest.hg19.template /opt/filer.ini

For working with the FILER data, you would also need schema/file format definitions for the various types of genomic tracks:

wget https://tf.lisanwanglab.org/GADB/metadata/filer.schemas.latest.tsv -P /mnt/data/FILER/

After installation of any of the FILER data through the metadata templates, please update filer.ini file and provide the absolute path for the root FILER directory and metadata, e.g.,

FILERDIR=/mnt/data/FILER/FILER_hg38
FILERMETADATA=/mnt/data/FILER/FILER_hg38/metadata/filer.latest.hg38.tsv
FILERTRACKSCHEMAS=/mnt/data/FILER/filer.schemas.latest.tsv

NOTE: you can create, e.g., a genome build-specific configuration file filer.hg38.ini and use it with all other FILER scripts.

For further details and example commands, e.g. for installing a custom subset of FILER data, please refer to the README (https://bitbucket.org/wanglab-upenn/FILER⁠).