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/
- Added new speciesman sources Andrea Guarracino (commit: GitHub) 5 years ago
- Added new sequencing technologies Andrea Guarracino (commit: GitHub) 5 years ago
- Added new countries Andrea Guarracino (commit: GitHub) 5 years ago
- Added new species and specimen sources Andrea Guarracino (commit: GitHub) 5 years ago
- Updated the host_sex and host_age management Andrea Guarracino (commit: GitHub) 5 years ago
- The NCBI Virus entries are updated automatically Andrea Guarracino (commit: GitHub) 5 years ago
- Virtuoso update in CRON Pjotr Prins 5 years ago
- Virtuoso uploader: always upload countries and labels Pjotr Prins 5 years ago
- Virtuoso: split named graphs Pjotr Prins 5 years ago
- Virtuoso uploader: does not delete graph yet Pjotr Prins 5 years ago
- Update graph script Pjotr Prins 5 years ago
- fixed UO_0000036 for year Andrea Guarracino (commit: GitHub) 5 years ago
- Merge pull request #41 from AndreaGuarracino/patch-14 LLTommy (commit: GitHub) 5 years ago
- Import script fixes Peter Amstutz 5 years ago
- Wrap import script to run as a workflow Peter Amstutz 5 years ago
- the date is now handled more formally Andrea Guarracino (commit: GitHub) 5 years ago
- Reverting country list back, something went wrong there lltommy 5 years ago
- updated to manage list fields and added new control on nasopharyngeal/throat swab Andrea Guarracino (commit: GitHub) 5 years ago
- Updated with new terms Andrea Guarracino (commit: GitHub) 5 years ago
- Updated with new terms Andrea Guarracino (commit: GitHub) 5 years ago
- Updated - 1731 IDs - 2020/04/28 Andrea Guarracino (commit: GitHub) 5 years ago
- Changes to the structure - we use lists now instead of strings where it makes sense. This allows us to have multiple values where in makes sense lltommy 5 years ago
- Updating dics lltommy 6 years ago
- Add script that updates Virtuoso - run as a CRON job Pjotr Prins 6 years ago
- Merge pull request #1 from AndreaGuarracino/patch-11 Andrea Guarracino (commit: GitHub) 6 years ago
- code cleaning, refactoring, submitter name and address Andrea Guarracino (commit: GitHub) 6 years ago
- added nasal swab for several new IDs Andrea Guarracino (commit: GitHub) 6 years ago
- updated IDs list - 2020/04/23 - 1436 IDs Andrea Guarracino (commit: GitHub) 6 years ago
- Adding a third sequence technology option lltommy 6 years ago
- Merge pull request #33 from AndreaGuarracino/patch-9 LLTommy (commit: GitHub) 6 years ago