How to run seqsender locally

Source: vignettes/local_installation.Rmd

SOFTWARE REQUIREMENTS:

  • Linux (64-bit) or Mac OS X (64-bit)
  • Git version 2.25.1 or later
  • Standard utilities: curl, tar, unzip

ADDITIONAL REQUIREMENTS:

See PRE-REQUISITES and REQUIREMENT FILES before proceeding to the next steps

Micromamba Installation

Here we recommend using micromamba to set up a virtual environment to run seqsender. Micromamba is a tiny, statically linked C++ reimplementation of mamba which is an alternative to conda. The tool works as a standalone package manager that supports a subset of all mamba or conda commands, but it also has its own separate command line interfaces. For more information, visit micromamba documentation.

To manually install, download and unzip the executable from the official conda-forge package to your $HOME directory using tar.

cd $HOME
  • LINUX
# Linux Intel (x86_64):
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
# Linux ARM64:
curl -Ls https://micro.mamba.pm/api/micromamba/linux-aarch64/latest | tar -xvj bin/micromamba
# Linux Power:
curl -Ls https://micro.mamba.pm/api/micromamba/linux-ppc64le/latest | tar -xvj bin/micromamba
  • macOS
# macOS Intel (x86_64):
curl -Ls https://micro.mamba.pm/api/micromamba/osx-64/latest | tar -xvj bin/micromamba
# macOS Silicon/M1 (ARM64):
curl -Ls https://micro.mamba.pm/api/micromamba/osx-arm64/latest | tar -xvj bin/micromamba

After the extraction is completed, you can find the executable at $HOME/bin/micromamba

  • To quickly use micromamba, you can simply run
export MAMBA_ROOT_PREFIX="$HOME/micromamba"
eval "$($HOME/bin/micromamba shell hook -s posix)"
  • To persist using micromamba, you can append the following script to your .bashrc (or .zshrc)
# >>> mamba initialize >>>
export MAMBA_EXE="$HOME/bin/micromamba";
export MAMBA_ROOT_PREFIX="$HOME/micromamba";
__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<
  • To check the current version of micromamba 
micromamba --version
1.5.6

Set up a micromamba environment

  1. Clone this repository to your $HOME directory
cd $HOME
git clone https://github.com/CDCgov/seqsender.git
  1. CD to seqsender folder where the env.yaml file is stored. Let’s create a virtual environment named mamba that contains all dependencies needed to run seqsender from the source file.
cd seqsender
micromamba create --name mamba --file env.yaml

  1. Activate the named environment – mamba 
micromamba activate mamba

Run seqsender within the mamba environment

First, let’s look a list of commands in seqsender. Currently, there are five implemented commands in seqsender: prep, submit, check_submission_status, template, version.

python seqsender.py --help


To see the arguments required for each command, for example, the submit command, run

python seqsender.py submit --help

Submit a test submission

Rather than hastily jump in and submit a production submission right away, we can utilize GISAID’s and NCBI’s “TEST-SERVER” to upload a test submission first. That way submitter can familiarize themselves with the submission process prior to make a real submission.

Note: Duplicate test submissions will result in an error. Please create new sequence names each time you plan to run test submissions to avoid this issue.

Submit a test submission with a pre-processed dataset

Submit a test submission with your own dataset




Any questions or issues? Please report them on our Github issue tracker.