Tree @master (Download .tar.gz)
- ..
- create_sra_metadata
- db_enrichment
- dict_ontology_standardization
- docker
- esr_samples
- submit_ebi
- update_virtuoso
- uthsc_samples
- cleanup.py
- delete_entries_on_arvados.py
- fetch_from_genbank.cwl
- foreach.sh
- import.cwl
- import_from_genbank.cwl
- import_to_arvados.py
- README.md
- split_into_arrays.cwl
- upload.cwl
- utils.py
Instructions for download and/or prepare the data and/or the metadata
Just go into the download_genbank_data or download_sra_data directory and execute the python3 script inside.
download_genbank_data/from_genbank_to_fasta_and_yaml.pydownloads the data and the matadata, preparing the FASTA and the YAML files;download_sra_data/download_sra_data.pycreates the metadata in the form of YAML files from the SraExperimentPackage.XXX.xml.gz file in the same directory.
History of
scripts
@master
git clone https://klaus.systemreboot.net/bh20-seq-resource/
- Jetson test sequence Pjotr Prins 5 years ago
- genbank: moving script into workflow space Pjotr Prins 5 years ago
- Ignores Pjotr Prins 5 years ago
- Genbank: comments Pjotr Prins 5 years ago
- added abPOA workflow; typos AndreaGuarracino 5 years ago
- removed provider_sample_id references AndreaGuarracino 5 years ago
- fix sequencing_coverage AndreaGuarracino 5 years ago
- fixed typos in the integer cast AndreaGuarracino 5 years ago
- added a check on host_age AndreaGuarracino 5 years ago
- added a check on host_age AndreaGuarracino 5 years ago
- check empty strings AndreaGuarracino 5 years ago
- fix check date sra script AndreaGuarracino 5 years ago
- generation of dates a little more robust AndreaGuarracino 5 years ago
- to not create YAML files with date before 2019 December AndreaGuarracino 5 years ago
- fix in the ids to consider AndreaGuarracino 5 years ago
- added ids-to-consider option to the NCBI script AndreaGuarracino 5 years ago
- managed the assembly_method in the scripts, doc, and the example templates AndreaGuarracino 5 years ago
- updated alignment_protocol field in the script, doc, and the example templates AndreaGuarracino 5 years ago
- Conflict in guix-deploy Pjotr Prins 5 years ago
- Deployment Pjotr Prins 5 years ago
- Move files to correct folder lltommy 5 years ago
- Merge branch 'master' of https://github.com/arvados/bh20-seq-resource lltommy 5 years ago
- Adding covid death and covid cases per country as additional background information lltommy 5 years ago
- create_sra_metadata script doesn't trick the quality control about missing date aymore AndreaGuarracino 5 years ago
- virtuoso: no-cache Pjotr Prins 5 years ago
- virtuoso: header change Pjotr Prins 5 years ago
- virtuoso: Added a --no-cache option Pjotr Prins 5 years ago
- Uploaded UTHSC sequences Pjotr Prins 5 years ago
- UTHSC samples Pjotr Prins 5 years ago
- Add country entries that miss coordinates Pjotr Prins 5 years ago