John Huddleston

nextstrain view can't connect to host on a Mac inside a Conda environment

8

### Current Behavior As of version 7.3.0.post1, I get the following error when trying to run `nextstrain view`: ```bash $ nextstrain view auspice [±master ●] Traceback (most recent call last):...

### Current Behavior When users run the `nextstrain build` command from Windows with Docker and provide an argument to Snakemake that references a local path using backslashes (e.g., `nextstrain build...

List previously submitted AWS Batch jobs in the job queue

2

## Context When a user submits a job to AWS Batch, they receive a job id they can use to reattach to the job later on. If the user doesn't...

### Context In addition to ferret serological data, we also now receive individual-level human serological data. These new data do not have the same columns and values as the ferret...

### Current Behavior Running fauna downloads with Python 3.10, I get the following error: ``` $ python3 ../fauna/vdb/download.py --database vdb --virus flu --fasta_fields strain virus accession collection_date virus_inclusion_date region country...

Allow ncov-ingest to download from non-AWS remote file paths

2

### Context To support running ingest on Terra, we need to support downloading existing Nextclade alignments and metadata from remote storage other than AWS's S3. ### Description We need to...

### Context Related to #307, we want to support users who run the ingest workflow on different cloud platforms like Google Cloud (for example, through Terra). Although we can bypass...

## Context The Snakemake workflow for ingest was written to map as directly from the original ingest shell scripts to Snakemake as possible. As a result, some of the workflow's...

For users who want to use GISAID data with this workflow, the following steps work _nearly_ as expected. These steps assume you have downloaded: - all sequences in FASTA format...

I originally plotted counts of HA sequences by lineage and region with altair, with the plan to make the figure interactive. However, we end up most often including these figures...