metscale

metscale copied to clipboard

Offline setup fails, cannot fetch Singularity images

7

I am downloading MetScale for the first time and am running into issues with the download of the Singularity images when I run python download_offline_files.py --workflow all **Error message** Downloading...

axiao19

Bumps [requests](https://github.com/psf/requests) from 2.24.0 to 2.31.0. Release notes Sourced from requests's releases. v2.31.0 2.31.0 (2023-05-22) Security Versions of Requests between v2.3.0 and v2.30.0 are vulnerable to potential forwarding of Proxy-Authorization...

dependabot[bot]

Add newer/additional Kraken DBs for DQT/taxasaurus rex

1

A colleague from the SV Hackathon 2022 shared a link with me to the updated kraken 2 databases, possible useful for the `DQT`/`taxasaurus rex` tool: [kraken2 indices](https://benlangmead.github.io/aws-indexes/k2) I don't have...

mtisza1

**Mike's suggestions for minor improvements on this script (`query_taxon_clades.py`):** 1. Change output file format and/or print the result in a more compact format ala the other tool 2. Query the...

mtisza1

See #11 and commentary therein. Another workflow, run after the `post_processing_move_samples_dir_workflow` workflow, could create the Rmarkdown source, replacing the sample ID parameter with the correct string, and then issuing the...

stephenturner

Do not require copying/linking/renaming input data

2

### Expected behavior The user should be able to invoke the metagenomics workflow from any arbitrary directory, assuming the correct absolute or relative path to relevant Snakefile(s) is indicated. The...

standage

Data directory is disorganized

2

### Expected behavior Clean organization of input/output data separated by sample (and preferably project) Separation of input/output data from reference data ### Actual behavior Unstructured data directory containing all input...

lovettse

Feature request: Higher-level workflows

1

As currently designed, there are 33 separate workflows organized into 5 categories. It would be nice to call higher-level workflows that performed all analyses in a given category or all...

lovettse

Can not download the mtsv_db

1

Hi, The code can not download the mtsv_db, the website seems need to login. python download_offline_files.py --workflow mtsv_db Downloading complete_genome.tar.gz from https://rcdata.nau.edu/fofanov_lab/Compressed_MTSV_database_files/complete_genome.tar.gz Error downloading file complete_genome.tar.gz Retry script. HTTP Error...

540889956