grabseqs - 1.0.0 - Fix SRA downloads

• Added a walk-through for adding a new repo using template.py
• Better handling for invalid SRA accession numbers
• Update endpoint for NCBI for SRA downloads
• Temporarily remove iMicrobe--needs rewrite to use a different tool

- Python
Published by louiejtaylor 7 months ago

grabseqs - 0.7.0 - Allow users to pass custom args to fast(er)q-dump

Version 0.7.0 consists of the following improvements: - Allow users to pass custom args to fast(er)q-dump - Minor re-writes of download handling code for easier readability

Thanks to an anonymous reviewer for this good suggestion!

- Python
Published by louiejtaylor about 6 years ago

grabseqs - 0.6.1 - Eliminate unnecessary warnings from pigz

Eliminate warnings from pigz for zipping files that don't exist by explicitly validating file existence beforehand (#34).

- Python
Published by louiejtaylor about 6 years ago

grabseqs - 0.6.0 - Gracefully handle incomplete or missing dependencies

- Python
Published by louiejtaylor about 6 years ago

grabseqs - 0.5.0 - Standardize metadata from all repositories

- Python
Published by louiejtaylor almost 7 years ago

grabseqs - Abstract functions to grabseqslib

- Python
Published by louiejtaylor about 7 years ago

grabseqs - Fix issue converting to .fastq from MG-RAST

- Python
Published by louiejtaylor about 7 years ago

grabseqs - More helpful error messages

- Python
Published by louiejtaylor about 7 years ago

grabseqs - Add helpful error messages when NCBI samples not found

- Python
Published by louiejtaylor about 7 years ago

grabseqs - Patch SRA downloading retries

Related to https://github.com/sunbeam-labs/sunbeam/issues/179

- Python
Published by louiejtaylor about 7 years ago

grabseqs - Allow user to not search NCBI for SRR#

(and just pass the SRR through). This will fix the problem where a single SRR was associated with multiple other SRRs, with no way to disambiguate them.

- Python
Published by louiejtaylor about 7 years ago

grabseqs - Add MG-RAST sample listing capability

- Python
Published by louiejtaylor over 7 years ago

grabseqs - Fix retries for SRA

- Python
Published by louiejtaylor over 7 years ago

grabseqs - Fix issue with clobber checking (and versions)

- Python
Published by louiejtaylor over 7 years ago

grabseqs - Fix issue with clobber checking

- Python
Published by louiejtaylor over 7 years ago

grabseqs - Fail more gracefully

- Python
Published by louiejtaylor over 7 years ago

grabseqs - Add flag for list-only, not download

- Python
Published by louiejtaylor over 7 years ago

grabseqs - MG-RAST downloading

- Python
Published by louiejtaylor over 7 years ago

grabseqs - Pass multiple project/sample accession numbers at once

- Python
Published by louiejtaylor over 7 years ago

grabseqs - v0.1 - Not pretty yet, but it works

- Python
Published by louiejtaylor over 7 years ago