From 24d173920a366f17f4b69f8f72ec45095cebadc3 Mon Sep 17 00:00:00 2001 From: Yangyang Li <yangyang.li@northwestern.edu> Date: Mon, 28 Oct 2024 21:46:29 -0500 Subject: [PATCH] Add: deepchopper (#51460) * Create meta.yaml of deepchopper * Update meta.yaml of deepchopper * Create build.sh of deepchopper * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * clean up recipe * add aarch64/arm64 builds * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml (evaluate do not have latest one) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com> Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/deepchopper/build.sh | 20 ++++++++++ recipes/deepchopper/meta.yaml | 74 +++++++++++++++++++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 recipes/deepchopper/build.sh create mode 100644 recipes/deepchopper/meta.yaml diff --git a/recipes/deepchopper/build.sh b/recipes/deepchopper/build.sh new file mode 100644 index 0000000000000..ba2ee9778318d --- /dev/null +++ b/recipes/deepchopper/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +# -e = exit on first error +# -x = print every executed command +set -ex + +# if [ `uname` == Darwin ]; then +# export HOME=`mktemp -d` +# fi + +curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y + +export PATH="$HOME/.cargo/bin:$PATH" +# export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC" +# export CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER="$CC" + + +maturin build --interpreter python --release + +$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv diff --git a/recipes/deepchopper/meta.yaml b/recipes/deepchopper/meta.yaml new file mode 100644 index 0000000000000..2e06be86b7c97 --- /dev/null +++ b/recipes/deepchopper/meta.yaml @@ -0,0 +1,74 @@ +{% set name = "deepchopper" %} +{% set version = "1.2.4" %} +{% set sha256 = "e7f0bfed8c34e011e924bc12e30dec9c58777f1879962b9a2036da29009461e4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [py < 310] + run_exports: + - {{ pin_subpackage("deepchopper", max_pin="x") }} + entry_points: + - deepchopper = deepchopper.cli:app + +requirements: + build: + - {{ compiler('rust') }} + - {{ compiler('c') }} + - make + - cmake + host: + - python + - pip + - maturin >=1.2.1,<2 + - setuptools-rust + - setuptools + run: + - python + - pytorch >=2.1.0 + - lightning >=2.1.2 + - torchmetrics >=1.2.0 + - rich >=13.7.0 + - transformers >=4.37.2 + - safetensors >=0.4.2 + - datasets ==2.14.2 + - evaluate >=0.4.1 + - typer >=0.12.0 + - gradio ==5.0.1 + - fastapi ==0.112.2 + - scikit-learn >=1.5.2 + - hydra-core >=1.3.2 + - omegaconf >=2.3.0 + - python-multipart ==0.0.12 + +test: + imports: + - deepchopper + commands: + - deepchopper --help + +about: + home: https://github.com/ylab-hi/DeepChopper + license: Apache-2.0 + license_family: Apache + license_file: LICENSE + summary: 'A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.' + description: | + DeepChopper is a genomic language model designed to identify artificial sequences. + It provides functionality for encoding FASTQ files, making predictions, and chopping sequences. + doc_url: https://github.com/ylab-hi/DeepChopper + dev_url: https://github.com/ylab-hi/DeepChopper + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - yangyangli