Installation¶
adaptiSeq is a Python package (Python ≥ 3.10) plus a small set of external command-line tools it shells out to.
1. Install with pip (recommended)¶
Note adaptiSeq is not yet on PyPI/bioconda. Until then, install from source (below).
2. Install from source¶
git clone https://github.com/swargo98/adaptiSeq.git
cd adaptiSeq
pip install -e . # editable / development install
pip install -e '.[test]' # + pytest, to run the test suite
adaptiseq --version
3. Conda environment¶
A conda environment file (environment.yml) is provided
that pulls both the external tools and the Python dependencies:
A dedicated bioconda package is TBD.
Python dependencies¶
Installed automatically by pip:
| Package | Why |
|---|---|
aiohttp (≥ 3.8) |
segmented HTTP(S) engine |
aioftp (≥ 0.21) |
native segmented FTP transport |
numpy (≥ 1.21) |
gradient adaptive-concurrency controller |
External command-line tools¶
adaptiSeq fetches metadata and runs integrity/conversion through a small set of external tools. Which ones you need depends on what you ask for:
| Tool | Needed for |
|---|---|
wget |
metadata / discovery (always) |
sra-tools (srapath, fasterq-dump, vdb-validate) |
SRA-fallback resolution, FASTQ conversion, md5/validation |
pigz |
gzip compression after conversion (-g/-q) |
md5sum (coreutils) |
md5 integrity checks (skipped with -k) |
axel |
only the opt-in classic engine with -p |
IBM ascp (Aspera) |
only -a |
adaptiSeq uses needs-based preflight: a pure ENA *.fastq.gz download needs
only wget — sra-tools and the rest are required (with a clear message) only
when a run actually takes a path that uses them. See the FAQ for the
exact messages and how to resolve them.