sqanti3-docker's Introduction

README

A docker image for running SQANTI3

Usage

There are two main Python scripts in SQANTI3: sqanti3_qc.py and sqanti3_RulesFilter.py. They can be run in the image as follows:

sqanti3_qc.py

# Using the most recent version
docker run --rm joelnitta/sqanti3:latest sqanti3_qc.py --help
# Using a specific version of SQANTI3
docker run --rm joelnitta/sqanti3:1.6.0 sqanti3_qc.py --help

sqanti3_RulesFilter.py

# Using the most recent version
docker run --rm joelnitta/sqanti3:latest sqanti3_RulesFilter.py --help
# Using a specific version of SQANTI3
docker run --rm joelnitta/sqanti3:1.6.0 sqanti3_RulesFilter.py --help

There are now three additional Python scripts in SQANTI3_protein: protein_classification.py, sample_and_ref_gtf_file_rename_cds_to_exon.py and sqanti3_protein.py. They can be run in the image as follows:

protein_classification.py

# Using the most recent version
docker run --rm adeslat/sqanti3-docker:latest protein_classification.py --help
# Using a specific version of SQANTI3
docker run --rm adeslat/sqanti3-docker:1.6.0 protein_classification.py --help

sample_and_ref_gtf_file_rename_cds_to_exon.py

# Using the most recent version
docker run --rm adeslat/sqanti3-docker:latest sample_and_ref_gtf_file_rename_cds_to_exon.py --help
# Using a specific version of SQANTI3
docker run --rm adeslat/sqanti3-docker:1.6.0 sample_and_ref_gtf_file_rename_cds_to_exon.py --help

sqanti3_protein.py

# Using the most recent version
docker run --rm adeslat/sqanti3-docker:latest sqanti3_protein.py --help
# Using a specific version of SQANTI3
docker run --rm adeslat/sqanti3-docker:1.6.0 sqanti3_protein.py --help

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