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ythuang0522 / homopolish

High-quality Nanopore-only genome polisher
GNU General Public License v3.0
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Conda installation- complications #62

Open JonathanAbrahams1337 opened 5 months ago

JonathanAbrahams1337 commented 5 months ago

Hi,

Excited to use modpolish. I am having trouble to install using conda/mamba though.

Installation using the command on the readme mamba create -n homopolish_mamba_auto_0_4_1 -c conda-forge -c bioconda homopolish installs version 0.3.3. This version doesnt have modpolish in.

When trying to specify the latest version 0.4.1 mamba create -n homopolish_mamba_auto_0_4_1 -c conda-forge -c bioconda homopolish==0.4.1 , this fails with the following:

Looking for: ['homopolish==0.4.1']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
pkgs/r/noarch                                                 No change
pkgs/main/linux-64                                            No change
pkgs/r/linux-64                                               No change
pkgs/main/noarch                                              No change
Could not solve for environment specs
Encountered problems while solving:
  - package homopolish-0.4.1-pyhdfd78af_0 requires libedit >=3.1.20210910, but none of the providers can be installed

The environment can't be solved, aborting the operation

And also trying to install 0.4 also fails.

Pohuii-Tzeng commented 5 months ago

Hello, It seems like you didn't change the channel priority to flexible. Maybe you can try running conda config --set channel_priority flexible before Installing homopolish. If there has no "defaults" channel in your conda info, like

channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
               https://repo.anaconda.com/pkgs/main/noarch
               https://repo.anaconda.com/pkgs/r/linux-64
               https://repo.anaconda.com/pkgs/r/noarch

you can try run mamba create -n homopolish_mamba_auto_0_4_1 -c conda-forge -c bioconda -c defaults homopolish==0.4.1 to install homopolish.

JonathanAbrahams1337 commented 5 months ago

Thanks for your fast response.

The mamba command ran succesfully, but I wasnt able to run homopolish uising it.

This is the environment I ended up with after running that mamba command and setting channels to flexbile.

name: homopolish_mamba_auto_0_4_1
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_kmp_llvm
  - arrow-cpp=3.0.0=py37h0161837_4_cpu
  - aws-c-cal=0.4.5=hb3cee0b_7
  - aws-c-common=0.5.1=h7f98852_0
  - aws-c-event-stream=0.2.7=hf6e4101_0
  - aws-c-io=0.9.0=hd4bc808_1
  - aws-checksums=0.1.11=hbd38b91_2
  - aws-sdk-cpp=1.8.138=hfa2f2a4_3
  - biopython=1.79=py37h540881e_2
  - blas=2.17=openblas
  - boost=1.70.0=py37h9de70de_1
  - boost-cpp=1.70.0=h7b93d67_3
  - brotli=1.1.0=hd590300_1
  - brotli-bin=1.1.0=hd590300_1
  - brotli-python=1.0.9=py37hd23a5d3_7
  - brotlipy=0.7.0=py37h540881e_1004
  - bzip2=1.0.8=hd590300_5
  - c-ares=1.27.0=hd590300_0
  - ca-certificates=2024.2.2=hbcca054_0
  - capnproto=1.0.2=hfc55251_0
  - certifi=2024.2.2=pyhd8ed1ab_0
  - cffi=1.15.1=py37h43b0acd_1
  - chardet=5.0.0=py37h89c1867_0
  - charset-normalizer=3.3.2=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - cryptography=38.0.2=py37h38fbfac_1
  - curl=7.87.0=h6312ad2_0
  - double-conversion=3.3.0=h59595ed_0
  - fastani=1.32=he1c1bb9_0
  - feather-format=0.4.1=pyh9f0ad1d_0
  - gflags=2.2.2=he1b5a44_1004
  - glog=0.4.0=h49b9bf7_3
  - grpc-cpp=1.35.0=h2157cd5_4
  - gsl=2.4=h294904e_1006
  - homopolish=0.4.1=pyhdfd78af_1
  - icu=67.1=he1b5a44_0
  - idna=3.6=pyhd8ed1ab_0
  - joblib=1.3.2=pyhd8ed1ab_0
  - k8=0.2.5=hdcf5f25_4
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.20.1=hf9c8cef_0
  - ld_impl_linux-64=2.40=h41732ed_0
  - libabseil=20230802.1=cxx17_h59595ed_0
  - libblas=3.8.0=17_openblas
  - libbrotlicommon=1.1.0=hd590300_1
  - libbrotlidec=1.1.0=hd590300_1
  - libbrotlienc=1.1.0=hd590300_1
  - libcblas=3.8.0=17_openblas
  - libcurl=7.87.0=h6312ad2_0
  - libdeflate=1.13=h166bdaf_0
  - libedit=3.1.20230828=h5eee18b_0
  - libev=4.33=hd590300_2
  - libevent=2.1.10=h9b69904_4
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=13.2.0=h807b86a_5
  - libgfortran-ng=7.5.0=h14aa051_20
  - libgfortran4=7.5.0=h14aa051_20
  - liblapack=3.8.0=17_openblas
  - liblapacke=3.8.0=17_openblas
  - libnghttp2=1.51.0=hdcd2b5c_0
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.10=pthreads_hb3c22a3_5
  - libprotobuf=3.14.0=h780b84a_0
  - libsqlite=3.45.1=h2797004_0
  - libssh2=1.10.0=haa6b8db_3
  - libstdcxx-ng=13.2.0=h7e041cc_5
  - libthrift=0.13.0=hbe8ec66_6
  - libutf8proc=2.8.0=h166bdaf_0
  - libzlib=1.2.13=hd590300_5
  - llvm-openmp=15.0.7=h0cdce71_0
  - lz4-c=1.9.3=h9c3ff4c_1
  - mash=2.1.1=he518ae8_0
  - minimap2=2.26=he4a0461_2
  - more-itertools=10.0.0=pyhd8ed1ab_0
  - ncbi-datasets-cli=16.6.0=ha770c72_0
  - ncurses=6.4=h59595ed_2
  - numpy=1.18.5=py37h8960a57_0
  - numpy-base=1.18.5=py37h2f8d375_0
  - openssl=1.1.1w=hd590300_0
  - orc=1.6.7=h7950760_0
  - pandas=1.3.5=py37he8f5f7f_0
  - parquet-cpp=1.5.1=2
  - pip=24.0=pyhd8ed1ab_0
  - pyarrow=3.0.0=py37h0ef46b9_4_cpu
  - pycparser=2.21=pyhd8ed1ab_0
  - pycurl=7.45.1=py37haaec8a5_2
  - pyopenssl=23.2.0=pyhd8ed1ab_1
  - pysam=0.21.0=py37hee149a5_0
  - pysocks=1.7.1=py37h89c1867_5
  - python=3.7.12=hb7a2778_100_cpython
  - python-dateutil=2.9.0=pyhd8ed1ab_0
  - python-wget=3.2=py_0
  - python_abi=3.7=4_cp37m
  - pytz=2024.1=pyhd8ed1ab_0
  - re2=2020.11.01=h58526e2_0
  - readline=8.2=h8228510_1
  - requests=2.31.0=pyhd8ed1ab_0
  - s2n=1.0.0=h9b69904_0
  - scikit-learn=0.21.3=py37hcdab131_0
  - scipy=1.5.3=py37h8911b10_0
  - setuptools=59.8.0=py37h89c1867_1
  - six=1.16.0=pyh6c4a22f_0
  - snappy=1.1.10=h9fff704_0
  - sqlite=3.45.1=h2c6b66d_0
  - thrift-compiler=0.13.0=hbe8ec66_6
  - thrift-cpp=0.13.0=6
  - tk=8.6.13=noxft_h4845f30_101
  - tqdm=4.66.2=pyhd8ed1ab_0
  - uriparser=0.9.7=h59595ed_1
  - urllib3=2.2.1=pyhd8ed1ab_0
  - wheel=0.42.0=pyhd8ed1ab_0
  - xz=5.2.6=h166bdaf_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.4.9=ha95c52a_0

I get this error when doing homopolish --help

Traceback (most recent call last):
  File "/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/bin/homopolish", line 6, in <module>
    from homopolish.homopolish import main
  File "/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/lib/python3.7/site-packages/homopolish/homopolish.py", line 4, in <module>
    from modules.polish_interface import polish_genome
  File "/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/lib/python3.7/site-packages/modules/polish_interface.py", line 11, in <module>
    from modules import polish
  File "/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/lib/python3.7/site-packages/modules/polish.py", line 5, in <module>
  File "/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/lib/python3.7/site-packages/more_itertools/__init__.py", line 3, in <module>
    from .more import *  # noqa
  File "/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/lib/python3.7/site-packages/more_itertools/more.py", line 5, in <module>
    from functools import cached_property, partial, reduce, wraps
ImportError: cannot import name 'cached_property' from 'functools' (/home/OXFORDNANOLABS/jabrahams/miniconda3/envs/homopolish_mamba_auto_0_4_1/lib/python3.7/functools.py)

I have managed to get the homopolymer part of the tool running smoothly with a custom environment and a few tweaks to the code, but the modpolish part doesnt work correctly in this env. So would very much appreciate your continued help with this! homopolish_homopolish_flexi_manual.txt

Pohuii-Tzeng commented 5 months ago

We found the "ImportError" is caused by the "more-itertools" version.

You can try using mamba create -n homopolish_env -c conda-forge -c bioconda -c defaults more-itertools=8.4.0 homopolish=0.4.1 homopolish==0.4.1 to specify the version of "more-itertools" and recreate the evironment.