From 70631818518705caaa90eda3bd5eafdceb761379 Mon Sep 17 00:00:00 2001 From: Gemy Kaithakottil Date: Mon, 11 Nov 2024 11:46:45 +0000 Subject: [PATCH] feat: harmonise conda dependencies and installation --- pyproject.toml | 2 +- reat.yml | 98 ++++++++++++++++++++++++++++++++++++++++++++++---- setup.py | 5 --- 3 files changed, 93 insertions(+), 12 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 84b8fcc..4e65910 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,2 +1,2 @@ [build-system] -requires = ["Cython", "numpy~=1.20.3", "setuptools", "wheel"] +requires = ["Cython", "numpy~=1.23.3", "setuptools", "wheel"] diff --git a/reat.yml b/reat.yml index d1c438f..665b8eb 100644 --- a/reat.yml +++ b/reat.yml @@ -1,16 +1,102 @@ name: REAT channels: - - conda-forge - bioconda + - conda-forge + - defaults + - anaconda dependencies: - - pip + - python>=3.9,<3.11 + - appdirs=1.4.4 + - attrs=22.1.0 + - biopython=1.79 + - brotlipy=0.7.0 + - bumpversion=0.5.3 + - certifi=2022.9.24 + - cffi=1.15.1 + - charset-normalizer=2.1.1 + - click=8.1.3 + - click-log=0.4.0 + - colorama=0.4.5 + - conda=22.9.0 + - conda-package-handling=1.9.0 + - ConfigArgParse=1.5.3 + - cryptography=37.0.1 + - Cython=0.29.32 + - datrie=0.8.2 + - docutils=0.19 + - drmaa=0.7.9 + - exceptiongroup=1.0.0rc9 + - filelock=3.8.0 + - gitdb=4.0.9 + - GitPython=3.1.29 + - greenlet=1.1.3.post0 + - hypothesis=6.56.2 + - idna=3.4 + - iniconfig=1.1.1 + - joblib=1.2.0 + - jsonschema=3.2.0 + - libmambapy=0.27.0 + - marshmallow=3.14.1 + - marshmallow-dataclass=8.5.3 + - msgpack-python==1.0.4 + - nbformat=5.7.0 + - ncls=0.0.65 + - networkx=2.8.7 + - numpy=1.23.3 + - packaging=21.3 + - pandas=1.5.0 + - pip=22.2.2 + - pluggy=1.0.0 + - psutil=5.9.2 + - PuLP=2.6.0 + - py=1.11.0 + - pycosat=0.6.3 + - pycparser=2.21 + - pyfaidx=0.5.9.5 + - pyOpenSSL=22.0.0 + - pyparsing=3.0.9 + - pyrsistent=0.18.1 + - pysam=0.19.1 + - PySocks=1.7.1 + - pytest=7.1.3 + - python-dateutil=2.8.2 + - python-rapidjson=1.9 + - pytz=2022.4 + - PyVCF3=1.0.3 + - PyYAML=6.0.1 + - requests=2.28.1 + - scikit-learn=1.1.2 + - scipy=1.11.1 + - setuptools=65.4.1 + - six=1.16.0 + - smart-open=6.2.0 + - snakemake=6.15.5 + - sortedcontainers=2.4.0 + - SQLAlchemy=1.4.41 + - SQLAlchemy-Utils=0.38.3 + - stopit=1.1.2 + - tabulate=0.9.0 + - threadpoolctl=3.1.0 + - toml=0.10.2 + - tomli=2.0.1 + - toolz=0.12.0 + - toposort=1.7 + - tqdm=4.64.1 + - traitlets=5.4.0 + - typeguard=2.13.3 + - typing_extensions=4.4.0 + - wheel=0.37.1 + - wrapt=1.14.1 + - samtools>=1.11 + - htslib>=1.11 + - prodigal==2.6.3 + - diamond==2.0.11 + - portcullis==1.2.4 - git=2.26.0 - gnuplot=5.4.1 - libjpeg-turbo=2.1.0 - bioawk=1.0 - seqkit=0.16.1 - - samtools=1.12 - - portcullis=1.2.4 - stringtie=2.1.5 - hisat2=2.2.1 - minimap2=2.18 @@ -21,9 +107,7 @@ dependencies: - gffread=0.12.1 - seqtk=1.3 - transdecoder=5.5.0 - - prodigal=2.6.3 - blast>=2.9.0 - - diamond>=2.0.0 - scallop-lr=0.9.2 - bedtools=2.30.0 - ucsc-wigtobigwig=377 @@ -32,3 +116,5 @@ dependencies: - codingquarry=2.0 - augustus=3.4.0 - evidencemodeler=1.1.1 + - miniprot=0.12 + diff --git a/setup.py b/setup.py index 54e1bb1..048be56 100644 --- a/setup.py +++ b/setup.py @@ -36,11 +36,6 @@ ), scripts=[script for script in glob.glob("annotation/scripts/*")], install_requires=[ - "biopython~=1.78", - "mikado~=2.3.4", - "pyfaidx~=0.5.8", - "jsonschema~=3.2.0", - "pyyaml~=5.4.1", "parasail~=1.2.4", "2passtools @ git+https://github.com/bartongroup/2passtools.git#d4378d0", ],