From 7f934114b0a49f8345d5c6e0ee7350250916b002 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Mon, 29 Jun 2026 23:04:29 +0930 Subject: [PATCH 1/3] Fix #98 add support for compressed files --- HISTORY.md | 1 + docs/run.md | 2 +- src/dnaapler/__init__.py | 31 +++++++++++++++++++++ src/dnaapler/utils/validation.py | 44 ++++++++++++++++++++++++++++++ tests/test_dnaapler.py | 46 ++++++++++++++++++++++++++++++++ tests/test_overall.py | 22 +++++++++++++++ 6 files changed, 145 insertions(+), 1 deletion(-) diff --git a/HISTORY.md b/HISTORY.md index 99ae868..afa7028 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,6 +2,7 @@ # 1.4.0 +* Adds support for gzip-, bzip2- and xz-compressed input ([#98](https://github.com/gbouras13/dnaapler/issues/98)). `dnaapler` now transparently decompresses `.gz`, `.bz2` and `.xz` input files (detected from the file's contents, regardless of extension), so compressed FASTA or GFA files can be passed directly to any subcommand. * Fixes [#102](https://github.com/gbouras13/dnaapler/issues/102). `dnaapler largest`, `mystery` and `nearest` could reorient to the wrong coordinate when the chosen CDS was on the negative strand, as the lowest coordinate of the CDS was used instead of its actual start codon. The reoriented sequence now correctly begins at the start codon. A related latent bug in the negative-strand fallback of the MMseqs2-based reorientation was also fixed. * If you run `dnaapler` with GFA input, it now also writes a `{prefix}_reoriented.fasta` alongside the `{prefix}_reoriented.gfa`. This FASTA contains all contigs from the GFA (circular contigs reoriented with overlap trimmed, non-circular contigs passed through unchanged), so it can be fed directly to downstream tools such as polishers. * If a GFA input contains no circular sequences, `dnaapler` no longer exits with an error. Instead it warns, copies the input GFA to the output, and writes all sequences out as a linear `{prefix}_reoriented.fasta`. For `dnaapler all` and `dnaapler bulk`, a reorientation summary is also written with every contig marked as not reoriented. diff --git a/docs/run.md b/docs/run.md index 89ee093..524fdbe 100644 --- a/docs/run.md +++ b/docs/run.md @@ -1,7 +1,7 @@ # Running `dnaapler` -For all subcommands, `dnaapler` requires an input FASTA file using the `-i` or `--input` parameters. +For all subcommands, `dnaapler` requires an input FASTA file using the `-i` or `--input` parameters. The input may be in FASTA or GFA format, and may be gzip (`.gz`), bzip2 (`.bz2`) or xz (`.xz`) compressed (this is detected automatically, regardless of the file extension). It is also highly recommended to specify an output directory using the `-o` or `--output` parameters, otherwise `dnaapler` will write the output to a directory named `output.dnaapler` by default. diff --git a/src/dnaapler/__init__.py b/src/dnaapler/__init__.py index d5e0a02..411b1cf 100755 --- a/src/dnaapler/__init__.py +++ b/src/dnaapler/__init__.py @@ -32,6 +32,7 @@ ) from dnaapler.utils.validation import ( check_evalue, + decompress_if_needed, instantiate_dirs, process_ignore_input, validate_choice_autocomplete, @@ -187,6 +188,9 @@ def chromosome( f"You have chosen {autocomplete} method to reorient your sequence if the MMseqs2 based method fails." ) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -271,6 +275,9 @@ def archaea( f"You have chosen {autocomplete} method to reorient your sequence if the MMseqs2 based method fails." ) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -355,6 +362,9 @@ def plasmid( f"You have chosen {autocomplete} method to reorient your sequence if the MMseqs2 based method fails." ) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -439,6 +449,9 @@ def phage( f"You have chosen {autocomplete} method to reorient your sequence if the MMseqs2 based method fails." ) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -530,6 +543,9 @@ def custom( f"You have chosen {autocomplete} method to reorient your sequence if the MMseqs2 based method fails." ) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -618,6 +634,9 @@ def mystery(ctx, input, output, threads, prefix, seed_value, force, **kwargs): # initial logging etc start_time = begin_dnaapler(input, output, threads, gene, params) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) @@ -658,6 +677,9 @@ def nearest(ctx, input, output, threads, prefix, force, **kwargs): # initial logging etc start_time = begin_dnaapler(input, output, threads, gene, params) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -707,6 +729,9 @@ def largest(ctx, input, output, threads, prefix, force, **kwargs): # initial logging etc start_time = begin_dnaapler(input, output, threads, gene, params) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input(input) input_is_gfa, input, original_gfa, gfa_no_circular = prep_gfa(input, output, prefix) @@ -799,6 +824,9 @@ def bulk( # initial logging etc start_time = begin_dnaapler(input, output, threads, gene, params) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input_bulk(input) check_duplicate_headers(input) @@ -977,6 +1005,9 @@ def all( # initial logging etc start_time = begin_dnaapler(input, output, threads, gene, params) + # decompress the input first if it is gzip/bzip2 compressed + input = decompress_if_needed(input, output) + # validates fasta or gfa validate_input_all(input) check_duplicate_headers(input) diff --git a/src/dnaapler/utils/validation.py b/src/dnaapler/utils/validation.py index 8d16f5b..a55323e 100644 --- a/src/dnaapler/utils/validation.py +++ b/src/dnaapler/utils/validation.py @@ -1,3 +1,8 @@ +import atexit +import bz2 +import gzip +import lzma +import os import re import shutil import sys @@ -40,6 +45,45 @@ def instantiate_dirs(output_dir: str, force: bool) -> None: Path(output_dir).mkdir(parents=True, exist_ok=True) +def decompress_if_needed(input_file: Path, output_dir: str) -> str: + """ + If input_file is gzip-, bzip2- or xz-compressed, decompress it to a temporary file in the output + directory and return that path; otherwise return input_file unchanged. Compression is detected + from the file's magic bytes, so it works regardless of the file extension. The temporary file is + removed automatically when dnaapler exits. + + This lets the rest of the pipeline (validation, GFA handling, Pyrodigal and MMseqs2) operate on + a plain uncompressed file without any of them needing to be compression-aware. + """ + with open(input_file, "rb") as handle: + magic = handle.read(6) + + if magic[:2] == b"\x1f\x8b": + opener = gzip.open + compression = "gzip" + elif magic[:3] == b"BZh": + opener = bz2.open + compression = "bzip2" + elif magic[:6] == b"\xfd7zXZ\x00": + opener = lzma.open + compression = "xz" + else: + return str(input_file) + + logger.info( + f"{input_file} appears to be {compression}-compressed; decompressing to a temporary file." + ) + decompressed = os.path.join(output_dir, "dnaapler_decompressed_input.fasta") + with opener(input_file, "rb") as src, open(decompressed, "wb") as dst: + shutil.copyfileobj(src, dst) + + # remove the temporary decompressed file when dnaapler exits + atexit.register( + lambda: os.remove(decompressed) if os.path.exists(decompressed) else None + ) + return decompressed + + def is_fasta(input_file): """ Check if the file is in FASTA format. diff --git a/tests/test_dnaapler.py b/tests/test_dnaapler.py index c90786c..b382a10 100755 --- a/tests/test_dnaapler.py +++ b/tests/test_dnaapler.py @@ -31,6 +31,7 @@ ) from src.dnaapler.utils.validation import ( check_evalue, + decompress_if_needed, validate_choice_autocomplete, validate_custom_db_fasta, validate_input, @@ -243,6 +244,51 @@ def test_run_largest_negative_strand(self, tmp_path=None): ) +class TestDecompressIfNeeded(unittest.TestCase): + """Tests for decompress_if_needed - issue #98 (compressed FASTA input).""" + + def _check_roundtrip(self, compressor, suffix): + import tempfile + + from Bio import SeqIO + + src = os.path.join(overall_inputs_test_data, "plasmid.fasta") + with tempfile.TemporaryDirectory() as tmp_dir: + compressed = os.path.join(tmp_dir, f"in.fasta{suffix}") + with open(src, "rb") as fh, compressor(compressed, "wb") as out: + out.write(fh.read()) + + result = decompress_if_needed(compressed, tmp_dir) + assert result != compressed, "expected a new decompressed path" + + original = [(r.id, str(r.seq)) for r in SeqIO.parse(src, "fasta")] + decompressed = [(r.id, str(r.seq)) for r in SeqIO.parse(result, "fasta")] + assert decompressed == original + + def test_gzip_input_decompressed(self): + import gzip + + self._check_roundtrip(gzip.open, ".gz") + + def test_bzip2_input_decompressed(self): + import bz2 + + self._check_roundtrip(bz2.open, ".bz2") + + def test_xz_input_decompressed(self): + import lzma + + self._check_roundtrip(lzma.open, ".xz") + + def test_plain_input_returned_unchanged(self): + import tempfile + + plain = os.path.join(overall_inputs_test_data, "plasmid.fasta") + with tempfile.TemporaryDirectory() as tmp_dir: + result = decompress_if_needed(plain, tmp_dir) + assert result == str(plain) + + class TestGfaToFasta(unittest.TestCase): """Tests for gfa_to_fasta - GFA input should yield a complete FASTA of all contigs.""" diff --git a/tests/test_overall.py b/tests/test_overall.py index c1cc81d..0e65770 100755 --- a/tests/test_overall.py +++ b/tests/test_overall.py @@ -286,6 +286,28 @@ def test_gfa_all(tmp_dir): assert "rotated=True" not in fasta_records["5"].description +def test_compressed_input(tmp_dir): + """gzipped FASTA input (issue #98) should give the same result as uncompressed input.""" + import gzip + + plain_input: Path = f"{overall_test_data}/plasmid.fasta" + gz_input = f"{tmp_dir}/plasmid.fasta.gz" + with open(plain_input, "rb") as fh, gzip.open(gz_input, "wb") as out: + out.write(fh.read()) + + plain_out = f"{tmp_dir}/compressed_plain" + gz_out = f"{tmp_dir}/compressed_gz" + exec_command(f"dnaapler plasmid -i {plain_input} -o {plain_out} -t 1 -f") + exec_command(f"dnaapler plasmid -i {gz_input} -o {gz_out} -t 1 -f") + + plain_seq = str( + next(SeqIO.parse(f"{plain_out}/dnaapler_reoriented.fasta", "fasta")).seq + ) + gz_seq = str(next(SeqIO.parse(f"{gz_out}/dnaapler_reoriented.fasta", "fasta")).seq) + assert len(gz_seq) > 0 + assert gz_seq == plain_seq + + def test_gfa_no_circular(tmp_dir): """test all with a GFA input that has no circular sequences - instead of erroring, dnaapler should warn, copy the input GFA to the output, and write all sequences out as a linear FASTA.""" From f243ba1e1f5ea4d92180ae5e0dda3715c14fd9b4 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Tue, 30 Jun 2026 09:25:12 +0930 Subject: [PATCH 2/3] pixi --- .gitattributes | 2 + .github/workflows/ci.yaml | 49 +- .github/workflows/release.yaml | 29 +- .gitignore | 4 + build/environment.yaml | 11 - justfile | 20 +- pixi.lock | 3915 ++++++++++++++++++++++++++++++++ poetry.lock | 810 ------- pyproject.toml | 86 +- requirements.txt | 9 - src/dnaapler/utils/VERSION | 2 +- 11 files changed, 4017 insertions(+), 920 deletions(-) create mode 100644 .gitattributes delete mode 100644 build/environment.yaml create mode 100644 pixi.lock delete mode 100644 poetry.lock delete mode 100644 requirements.txt diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 565d7df..00ca90d 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -1,52 +1,33 @@ name: CI -on: [push,pull_request] +on: [push, pull_request] jobs: tests: - name: "Python ${{ matrix.python-version }}" + name: "Tests (${{ matrix.os }})" runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash -el {0} - strategy: matrix: os: [macos-latest, ubuntu-latest] - python-version: ["3.9"] steps: - - uses: "actions/checkout@v3" + - uses: actions/checkout@v4 with: fetch-depth: 0 - # Setup env - - uses: conda-incubator/setup-miniconda@v3 + - name: Setup Pixi + uses: prefix-dev/setup-pixi@v0.8.1 with: - activate-environment: dnaapler - environment-file: build/environment.yaml - python-version: ${{ matrix.python-version }} - auto-activate-base: false - channels: conda-forge,bioconda,defaults - channel-priority: strict - auto-update-conda: true - - name: Install project - shell: bash -l {0} - run: | - conda install python=${{ matrix.python-version }} pip - python -m pip install --upgrade pip - pip install -e . - pip install ruff - pip install pytest - pip install pytest-cov - - name: Check formatting - shell: bash -l {0} - run: just check-fmt - - name: Test and generate coverage report with pytest - shell: bash -l {0} - run: just test-ci + pixi-version: v0.71.2 + cache: true + environments: dev + + - name: Check formatting and lint + run: pixi run check-fmt + + - name: Run unit tests + run: pixi run test-ci + - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v4 - - diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 4754605..5487ca4 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -11,27 +11,20 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: conda-incubator/setup-miniconda@v3 + - uses: actions/checkout@v4 + + - name: Setup Pixi + uses: prefix-dev/setup-pixi@v0.8.1 with: - python-version: 3.9 - activate-environment: dnaapler - environment-file: build/environment.yaml - auto-activate-base: false - channels: conda-forge,bioconda,defaults - channel-priority: strict - auto-update-conda: true - - name: Install project - shell: bash -l {0} - run: | - python -m pip install -U pip - pip install -e . - pip install ruff + pixi-version: v0.71.2 + cache: true + environments: dev + - name: Build a binary wheel and a source tarball - shell: bash -l {0} - run: just build + run: pixi run build + - name: Publish to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ - password: ${{ secrets.PYPI_TOKEN }} \ No newline at end of file + password: ${{ secrets.PYPI_TOKEN }} diff --git a/.gitignore b/.gitignore index 279fa4a..fa35f21 100644 --- a/.gitignore +++ b/.gitignore @@ -110,3 +110,7 @@ ENV/ .DS_Store */.DS_Store */*/.DS_Store + +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/build/environment.yaml b/build/environment.yaml deleted file mode 100644 index bffb51e..0000000 --- a/build/environment.yaml +++ /dev/null @@ -1,11 +0,0 @@ -name: dnaapler_env -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - mmseqs2 >=13.45111 - - just - - poetry - - python >=3.8,<4.0 - - ripgrep \ No newline at end of file diff --git a/justfile b/justfile index 1cee4f6..03a256a 100644 --- a/justfile +++ b/justfile @@ -1,33 +1,31 @@ PROJECT := "dnaapler" OPEN := if os() == "macos" { "open" } else { "xdg-open" } -VERSION := `poetry version | rg -o '\d+\.\d+\.\d+'` +VERSION := `pixi workspace version get` # format code with ruff fmt: - poetry run ruff format . - poetry run ruff check --fix . + pixi run fmt # check formatting and lint with ruff check-fmt: - poetry run ruff format --check . - poetry run ruff check . + pixi run check-fmt -# install latest version with poetry +# install environment with pixi install: - poetry install --no-interaction + pixi install # run all tests test opts="": - poetry run pytest -vv {{opts}} tests/ + pixi run test {{opts}} # run tests with coverage report coverage: - poetry run pytest --cov-report term --cov-report html --cov={{ PROJECT }} --cov-branch tests/ + pixi run coverage {{ OPEN }} htmlcov/index.html # run tests on the CI test-ci: - poetry run pytest --cov={{ PROJECT }} --cov-report=xml --cov-branch tests/ + pixi run test-ci # prints out the commands to run to tag the release and push it tag: @@ -36,4 +34,4 @@ tag: # build a python release build: - poetry build --no-interaction \ No newline at end of file + pixi run build diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..04ca734 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,3915 @@ +version: 7 +platforms: +- name: linux-64 + virtual-packages: + - __unix=0=0 + - __linux=4.18 + - __glibc=2.28 + - __archspec=0=x86_64 +- name: osx-64 + virtual-packages: + - __unix=0=0 + - __osx=13.0 + - __archspec=0=x86_64 +- name: osx-arm64 + virtual-packages: + - __unix=0=0 + - __osx=13.0 + - __archspec=0=m1 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/bioconda/linux-64/mmseqs2-18.8cc5c-hd6d6fdc_0.tar.bz2 + - conda: https://conda.anaconda.org/bioconda/linux-64/pyrodigal-3.7.1-py313h8c92656_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aria2-1.37.0-h4b33fff_4.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/biopython-1.87-py313h07c4f96_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda + - 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"HISTORY.md" +requires-python = ">=3.8,<4.0" +dependencies = [ + "click>=8.0.0", + "loguru>=0.5.3", + "pyyaml>=6.0", + "pandas>=1.4.2", + "biopython>=1.76", + "pyrodigal>=3.0.0", ] -[tool.poetry.scripts] -dnaapler = 'dnaapler:main' +[project.urls] +homepage = "https://github.com/gbouras13/dnaapler" +repository = "https://github.com/gbouras13/dnaapler" + +[project.scripts] +dnaapler = "dnaapler:main" + +[tool.hatch.build.targets.wheel] +packages = ["src/dnaapler"] -[tool.poetry.dependencies] +[tool.ruff] +line-length = 88 +exclude = ["*.ipynb"] + +[tool.ruff.lint] +select = ["E", "F", "W", "I"] +ignore = ["E501"] + +[tool.pixi.workspace] +channels = ["conda-forge", "bioconda"] +platforms = ["linux-64", "osx-64", "osx-arm64"] + +[tool.pixi.dependencies] python = ">=3.8,<4.0" click = ">=8.0.0" loguru = ">=0.5.3" @@ -23,26 +52,31 @@ pyyaml = ">=6.0" pandas = ">=1.4.2" biopython = ">=1.76" pyrodigal = ">=3.0.0" +mmseqs2 = ">=13.45111" +[tool.pixi.pypi-dependencies] +dnaapler = { path = ".", editable = true } -[tool.poetry.dev-dependencies] -ruff = ">=0.4.0" +[tool.pixi.feature.test.dependencies] pytest = ">=6.2.5" pytest-cov = ">=3.0.0" -[[tool.poetry.source]] -name = "pypi-test" -url = "https://test.pypi.org/simple/" -priority = "primary" +[tool.pixi.feature.lint.dependencies] +ruff = ">=0.4.0" +hatch = "*" -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +[tool.pixi.feature.dev-tools.dependencies] +just = "*" +ripgrep = "*" -[tool.ruff] -line-length = 88 -exclude = ["*.ipynb"] +[tool.pixi.environments] +default = { solve-group = "default" } +dev = { features = ["test", "lint", "dev-tools"], solve-group = "default" } -[tool.ruff.lint] -select = ["E", "F", "W", "I"] -ignore = ["E501"] +[tool.pixi.tasks] +fmt = { cmd = "ruff format . && ruff check --fix .", default-environment = "dev" } +check-fmt = { cmd = "ruff format --check . && ruff check .", default-environment = "dev" } +test = { cmd = "pytest -vv tests/", default-environment = "dev" } +test-ci = { cmd = "pytest --cov=dnaapler --cov-report=xml --cov-branch tests/", default-environment = "dev" } +coverage = { cmd = "pytest --cov-report term --cov-report html --cov=dnaapler --cov-branch tests/", default-environment = "dev" } +build = { cmd = "hatch build", default-environment = "dev" } diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 1a31be7..0000000 --- a/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -pyyaml >=6.0 -pytest-runner >= 5.0.0 -biopython >=1.76 -pytest >=6.2.5 -pandas >=1.4.1 -loguru >=0.5.3 -Click >=8.0.0 -pytest-cov >=3.0.0 -pyrodigal >=2.0.0 diff --git a/src/dnaapler/utils/VERSION b/src/dnaapler/utils/VERSION index 589268e..e21e727 100644 --- a/src/dnaapler/utils/VERSION +++ b/src/dnaapler/utils/VERSION @@ -1 +1 @@ -1.3.0 \ No newline at end of file +1.4.0 \ No newline at end of file From ff305686b90ae91aa4d3635e7fa2630c234e493a Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Tue, 30 Jun 2026 09:57:28 +0930 Subject: [PATCH 3/3] Add pixi global install instructions to README Documents `pixi global install dnaapler` as a recommended installation method (alongside conda and pip), following #104. Co-Authored-By: Claude Opus 4.8 --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f81d332..16274d6 100644 --- a/README.md +++ b/README.md @@ -121,6 +121,7 @@ If you don't want to install `dnaapler` locally, you can run `dnaapler all` with - [Documentation](#documentation) - [Commands](#commands) - [Installation](#installation) + - [Pixi](#pixi) - [Conda](#conda) - [Pip](#pip) - [Usage](#usage) @@ -177,7 +178,15 @@ The full documentation for `dnaapler` can be found [here](https://dnaapler.readt `dnaapler` requires only `MMseqs2 v13.45111` as an external dependency. -Installation from conda is highly recommended as this will install `MMseqs2` automatically. +Installation using `pixi` or `conda` is highly recommended as this will install `MMseqs2` automatically. + +### Pixi + +`dnaapler` is available on bioconda and can be installed globally using `pixi`: + +``` +pixi global install dnaapler +``` ### Conda