From 53d9243e64f89a2c1572f084513d9fedc779240b Mon Sep 17 00:00:00 2001 From: Eric Kofman Date: Mon, 2 Jun 2025 18:37:38 -0700 Subject: [PATCH 1/2] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 3814d57..e49bde7 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,7 @@ Linux: Ubuntu 24.04.2 ## Python Dependencies -MARINE uses Python >= 3.8.18, and all required dependencies can be installed using the conda or mamba commands described below. +MARINE uses Python >= 3.10, and all required dependencies can be installed using the conda or mamba commands described below. # Installation Simply git clone this repository using the link at the top right on the main repository page. Should take at most a minute or two. @@ -50,8 +50,8 @@ Simply git clone this repository using the link at the top right on the main rep git clone https://github.com/YeoLab/MARINE.git ``` -MARINE was developed and tested using Python 3.8.18 and is not guaranteed to work with earlier versions of Python. -Use the provided .yml file to create a new conda environment that contains all required dependencies, including the proper Python version, for MARINE: +MARINE was developed and tested using Python 3.10 and is not guaranteed to work with earlier versions of Python. +Use the provided .yaml file (marine_environment2.yaml) to create a new conda environment that contains all required dependencies, including the proper Python version, for MARINE: ``` conda env create --file=marine_environment2.yaml From f7fdab8cef70c1c384df5df6cc188172c9ee342e Mon Sep 17 00:00:00 2001 From: Eric Kofman Date: Mon, 2 Jun 2025 18:38:34 -0700 Subject: [PATCH 2/2] Delete marine_environment_3_10.yml --- marine_environment_3_10.yml | 139 ------------------------------------ 1 file changed, 139 deletions(-) delete mode 100644 marine_environment_3_10.yml diff --git a/marine_environment_3_10.yml b/marine_environment_3_10.yml deleted file mode 100644 index 1b212fa..0000000 --- a/marine_environment_3_10.yml +++ /dev/null @@ -1,139 +0,0 @@ -name: marine_environment_3_10 -channels: - - anaconda - - conda-forge - - bioconda - - r - - defaults -dependencies: - - matplotlib - - pybedtools - - _libgcc_mutex - - _openmp_mutex - - abseil-cpp - - arrow-cpp - - asttokens - - aws-c-common - - aws-c-event-stream - - aws-checksums - - aws-sdk-cpp - - backcall - - backports - - backports.zoneinfo - - blas - - boost-cpp - - bottleneck - - brotli-python - - bzip2 - - c-ares - - ca-certificates - - certifi - - cffi - - charset-normalizer - - colorama - - comm - - cryptography - - debugpy - - decorator - - executing - - gflags - - glog - - grpc-cpp - - icu - - idna - - importlib-metadata - - importlib_metadata - - intel-openmp - - ipykernel - - ipython - - jedi - - jupyter_client - - jupyter_core - - krb5 - - ld_impl_linux-64 - - libbrotlicommon - - libbrotlidec - - libbrotlienc - - libcurl - - libdeflate - - libedit - - libev - - libevent - - libffi - - libgcc-ng - - libgfortran-ng - - libgfortran5 - - libgomp - - libnghttp2 - - libnsl - - libprotobuf - - libsodium - - libsqlite - - libssh2 - - libstdcxx-ng - - libthrift - - libuuid - - libzlib - - lz4-c - - matplotlib-inline - - mkl - - mkl-service - - mkl_fft - - mkl_random - - ncurses - - nest-asyncio - - numexpr - - numpy - - numpy-base - - openssl - - orc - - packaging - - pandas - - parso - - pexpect - - pickleshare - - pip - - platformdirs - - polars - - pooch - - prompt-toolkit - - psutil - - ptyprocess - - pure_eval - - pyarrow - - pycparser - - pygments - - pyopenssl - - pysam - - pysocks - - python - - python-dateutil - - python-tzdata - - python_abi - - pytz - - pyzmq - - re2 - - readline - - requests - - scalene - - scipy - - setuptools - - six - - snappy - - stack_data - - tbb - - tk - - tornado - - tqdm - - traitlets - - typing_extensions - - tzdata - - urllib3 - - utf8proc - - wcwidth - - wheel - - xz - - zeromq - - zipp - - zlib - - zstd \ No newline at end of file