LEAP installation error

[dianacornejo]

Hello LEAP developers,
I'm trying to install LEAP to be able to run Fast-LMM using binary traits for interaction analysis. However, I'm having a hard time installing LEAP. Any help is appreciated!

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Requirement already satisfied: leap_gwas in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/leap_gwas-0.1.7.2-py2.7.egg (0.1.7.2)
Requirement already satisfied: numpy in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (1.16.6)
Requirement already satisfied: scipy in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (1.2.3)
Collecting fastlmm
  Using cached https://files.pythonhosted.org/packages/4e/62/6bd368f9f7b7b3d2cc3d184c7f2f97d509a8402bb80dd51f135d1dc98857/fastlmm-0.4.8.tar.gz
  Installing build dependencies ... done
  WARNING: Missing build requirements in pyproject.toml for fastlmm from https://files.pythonhosted.org/packages/4e/62/6bd368f9f7b7b3d2cc3d184c7f2f97d509a8402bb80dd51f135d1dc98857/fastlmm-0.4.8.tar.gz#sha256=a3fb5c0468fb2978543d606d651292684943dd0fe66c975634ea17ea861823f1 (from leap_gwas).
  WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
    Preparing wheel metadata ... done
Requirement already satisfied: scikit-learn in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (0.20.4)
Requirement already satisfied: pandas in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (0.24.2)
Collecting statsmodels>=0.10.1
  Using cached https://files.pythonhosted.org/packages/53/1c/b83f6a4632b502a20b0f83bc5c25ebfa03eebd00efe9b45fcdcde1a0ab40/statsmodels-0.11.0.tar.gz
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting psutil>=5.6.7
  Using cached https://files.pythonhosted.org/packages/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz
Collecting matplotlib>=1.5.1
  Using cached https://files.pythonhosted.org/packages/9d/40/5ba7d4a3f80d39d409f21899972596bf62c8606f1406a825029649eaa439/matplotlib-2.2.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pysnptools>=0.4.10
  Using cached https://files.pythonhosted.org/packages/29/6e/430a65ae359c52571878f045b481693f30c151302e410480fece8f62db25/pysnptools-0.4.20.tar.gz
  Installing build dependencies ... done
  WARNING: Missing build requirements in pyproject.toml for pysnptools>=0.4.10 from https://files.pythonhosted.org/packages/29/6e/430a65ae359c52571878f045b481693f30c151302e410480fece8f62db25/pysnptools-0.4.20.tar.gz#sha256=f1d007e02d3581e558f35a2bd53ed92cd9678d5326afb463f12047b9b26516c2 (from fastlmm->leap_gwas).
  WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
    Preparing wheel metadata ... done
Collecting dill>=0.2.9
  Using cached https://files.pythonhosted.org/packages/e2/96/518a8ea959a734b70d2e95fef98bcbfdc7adad1c1e5f5dd9148c835205a5/dill-0.3.2.zip
Requirement already satisfied: pytz>=2011k in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from pandas->leap_gwas) (2020.1)
Requirement already satisfied: python-dateutil>=2.5.0 in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from pandas->leap_gwas) (2.8.1)
Collecting patsy>=0.5
  Using cached https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl
Collecting subprocess32
  Using cached https://files.pythonhosted.org/packages/93/dc/3a0ae313f1cf0f59b582e8e14891196e51fca5db193558b7661bd32b8801/subprocess32-3.5.4-cp27-cp27mu-manylinux2014_x86_64.whl
Collecting cycler>=0.10
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10 in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from matplotlib>=1.5.1->fastlmm->leap_gwas) (1.15.0)
Collecting backports.functools-lru-cache
  Using cached https://files.pythonhosted.org/packages/da/d1/080d2bb13773803648281a49e3918f65b31b7beebf009887a529357fd44a/backports.functools_lru_cache-1.6.1-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Using cached https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1
  Using cached https://files.pythonhosted.org/packages/3d/78/cb9248b2289ec31e301137cedbe4ca503a74ca87f88cdbfd2f8be52323bf/kiwisolver-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting h5py>=2.10.0
  Using cached https://files.pythonhosted.org/packages/12/90/3216b8f6d69905a320352a9ca6802a8e39fdb1cd93133c3d4163db8d5f19/h5py-2.10.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting bgen-reader>=4.0.4
  Using cached https://files.pythonhosted.org/packages/ef/f4/2775ad723b7011603ea1a3ca7021a554465e3175eaa1499590b11960fce7/bgen-reader-4.0.6.tar.gz
  Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/bin/python /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-x8e5wp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=49.3.0' 'wheel>=0.34.2'
       cwd: None
  Complete output (3 lines):
  DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
  ERROR: Could not find a version that satisfies the requirement setuptools>=49.3.0 (from versions: 0.6b1, 0.6b2, 0.6b3, 0.6b4, 0.6rc1, 0.6rc2, 0.6rc3, 0.6rc4, 0.6rc5, 0.6rc6, 0.6rc7, 0.6rc8, 0.6rc9, 0.6rc10, 0.6rc11, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.9.7, 0.9.8, 1.0, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.1.6, 1.1.7, 1.2, 1.3, 1.3.1, 1.3.2, 1.4, 1.4.1, 1.4.2, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.2, 3.0, 3.0.1, 3.0.2, 3.1, 3.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5, 3.5.1, 3.5.2, 3.6, 3.7, 3.7.1, 3.8, 3.8.1, 4.0, 4.0.1, 5.0, 5.0.1, 5.0.2, 5.1, 5.2, 5.3, 5.4, 5.4.1, 5.4.2, 5.5, 5.5.1, 5.6, 5.7, 5.8, 6.0.1, 6.0.2, 6.1, 7.0, 8.0, 8.0.1, 8.0.2, 8.0.3, 8.0.4, 8.1, 8.2, 8.2.1, 8.3, 9.0, 9.0.1, 9.1, 10.0, 10.0.1, 10.1, 10.2, 10.2.1, 11.0, 11.1, 11.2, 11.3, 11.3.1, 12.0, 12.0.1, 12.0.2, 12.0.3, 12.0.4, 12.0.5, 12.1, 12.2, 12.3, 12.4, 13.0.1, 13.0.2, 14.0, 14.1, 14.1.1, 14.2, 14.3, 14.3.1, 15.0, 15.1, 15.2, 16.0, 17.0, 17.1, 17.1.1, 18.0, 18.0.1, 18.1, 18.2, 18.3, 18.3.1, 18.3.2, 18.4, 18.5, 18.6, 18.6.1, 18.7, 18.7.1, 18.8, 18.8.1, 19.0, 19.1, 19.1.1, 19.2, 19.3, 19.4, 19.4.1, 19.5, 19.6, 19.6.1, 19.6.2, 19.7, 20.0, 20.1, 20.1.1, 20.2.2, 20.3, 20.3.1, 20.4, 20.6.6, 20.6.7, 20.6.8, 20.7.0, 20.8.0, 20.8.1, 20.9.0, 20.10.1, 21.0.0, 21.1.0, 21.2.0, 21.2.1, 21.2.2, 22.0.0, 22.0.1, 22.0.2, 22.0.4, 22.0.5, 23.0.0, 23.1.0, 23.2.0, 23.2.1, 24.0.0, 24.0.1, 24.0.2, 24.0.3, 24.1.0, 24.1.1, 24.2.0, 24.2.1, 24.3.0, 24.3.1, 25.0.0, 25.0.1, 25.0.2, 25.1.0, 25.1.1, 25.1.2, 25.1.3, 25.1.4, 25.1.5, 25.1.6, 25.2.0, 25.3.0, 25.4.0, 26.0.0, 26.1.0, 26.1.1, 27.0.0, 27.1.0, 27.1.2, 27.2.0, 27.3.0, 27.3.1, 28.0.0, 28.1.0, 28.2.0, 28.3.0, 28.4.0, 28.5.0, 28.6.0, 28.6.1, 28.7.0, 28.7.1, 28.8.0, 28.8.1, 29.0.0, 29.0.1, 30.0.0, 30.1.0, 30.2.0, 30.2.1, 30.3.0, 30.4.0, 31.0.0, 31.0.1, 32.0.0, 32.1.0, 32.1.1, 32.1.2, 32.1.3, 32.2.0, 32.3.0, 32.3.1, 33.1.0, 33.1.1, 34.0.0, 34.0.1, 34.0.2, 34.0.3, 34.1.0, 34.1.1, 34.2.0, 34.3.0, 34.3.1, 34.3.2, 34.3.3, 34.4.0, 34.4.1, 35.0.0, 35.0.1, 35.0.2, 36.0.1, 36.1.0, 36.1.1, 36.2.0, 36.2.1, 36.2.2, 36.2.3, 36.2.4, 36.2.5, 36.2.6, 36.2.7, 36.3.0, 36.4.0, 36.5.0, 36.6.0, 36.6.1, 36.7.0, 36.7.1, 36.7.2, 36.8.0, 37.0.0, 38.0.0, 38.1.0, 38.2.0, 38.2.1, 38.2.3, 38.2.4, 38.2.5, 38.3.0, 38.4.0, 38.4.1, 38.5.0, 38.5.1, 38.5.2, 38.6.0, 38.6.1, 38.7.0, 39.0.0, 39.0.1, 39.1.0, 39.2.0, 40.0.0, 40.1.0, 40.1.1, 40.2.0, 40.3.0, 40.4.0, 40.4.1, 40.4.2, 40.4.3, 40.5.0, 40.6.0, 40.6.1, 40.6.2, 40.6.3, 40.7.0, 40.7.1, 40.7.2, 40.7.3, 40.8.0, 40.9.0, 41.0.0, 41.0.1, 41.1.0, 41.2.0, 41.3.0, 41.4.0, 41.5.0, 41.5.1, 41.6.0, 42.0.0, 42.0.1, 42.0.2, 43.0.0, 44.0.0, 44.1.0, 44.1.1)
  ERROR: No matching distribution found for setuptools>=49.3.0
  ----------------------------------------
ERROR: Command errored out with exit status 1: /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/bin/python /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-x8e5wp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=49.3.0' 'wheel>=0.34.2' Check the logs for full command output.

This is the error message. I have tried to update steuptools to newer version but it does not seem to work. Is it possible to install LEAP using python 3. Thank you

[omerwe]

Hi, The problem seems to be associated with the fastlmm package, which is no longer maintained. I suggest you try to use a newer tool such as SAIGE for analyzing binary traits. Best, Omer

…

On Wed, Sep 23, 2020 at 9:18 PM diana.cornejo ***@***.***> wrote: Hello LEAP developers, I'm trying to install LEAP to be able to run Fast-LMM using binary traits for interaction analysis. However, I'm having a hard time installing LEAP. Any help is appreciated! DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Requirement already satisfied: leap_gwas in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/leap_gwas-0.1.7.2-py2.7.egg (0.1.7.2) Requirement already satisfied: numpy in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (1.16.6) Requirement already satisfied: scipy in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (1.2.3) Collecting fastlmm Using cached https://files.pythonhosted.org/packages/4e/62/6bd368f9f7b7b3d2cc3d184c7f2f97d509a8402bb80dd51f135d1dc98857/fastlmm-0.4.8.tar.gz Installing build dependencies ... done WARNING: Missing build requirements in pyproject.toml for fastlmm from https://files.pythonhosted.org/packages/4e/62/6bd368f9f7b7b3d2cc3d184c7f2f97d509a8402bb80dd51f135d1dc98857/fastlmm-0.4.8.tar.gz#sha256=a3fb5c0468fb2978543d606d651292684943dd0fe66c975634ea17ea861823f1 (from leap_gwas). WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'. Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing wheel metadata ... done Requirement already satisfied: scikit-learn in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (0.20.4) Requirement already satisfied: pandas in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (0.24.2) Collecting statsmodels>=0.10.1 Using cached https://files.pythonhosted.org/packages/53/1c/b83f6a4632b502a20b0f83bc5c25ebfa03eebd00efe9b45fcdcde1a0ab40/statsmodels-0.11.0.tar.gz Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Collecting psutil>=5.6.7 Using cached https://files.pythonhosted.org/packages/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz Collecting matplotlib>=1.5.1 Using cached https://files.pythonhosted.org/packages/9d/40/5ba7d4a3f80d39d409f21899972596bf62c8606f1406a825029649eaa439/matplotlib-2.2.5-cp27-cp27mu-manylinux1_x86_64.whl Collecting pysnptools>=0.4.10 Using cached https://files.pythonhosted.org/packages/29/6e/430a65ae359c52571878f045b481693f30c151302e410480fece8f62db25/pysnptools-0.4.20.tar.gz Installing build dependencies ... done WARNING: Missing build requirements in pyproject.toml for pysnptools>=0.4.10 from https://files.pythonhosted.org/packages/29/6e/430a65ae359c52571878f045b481693f30c151302e410480fece8f62db25/pysnptools-0.4.20.tar.gz#sha256=f1d007e02d3581e558f35a2bd53ed92cd9678d5326afb463f12047b9b26516c2 (from fastlmm->leap_gwas). WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'. Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing wheel metadata ... done Collecting dill>=0.2.9 Using cached https://files.pythonhosted.org/packages/e2/96/518a8ea959a734b70d2e95fef98bcbfdc7adad1c1e5f5dd9148c835205a5/dill-0.3.2.zip Requirement already satisfied: pytz>=2011k in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from pandas->leap_gwas) (2020.1) Requirement already satisfied: python-dateutil>=2.5.0 in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from pandas->leap_gwas) (2.8.1) Collecting patsy>=0.5 Using cached https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl Collecting subprocess32 Using cached https://files.pythonhosted.org/packages/93/dc/3a0ae313f1cf0f59b582e8e14891196e51fca5db193558b7661bd32b8801/subprocess32-3.5.4-cp27-cp27mu-manylinux2014_x86_64.whl Collecting cycler>=0.10 Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl Requirement already satisfied: six>=1.10 in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from matplotlib>=1.5.1->fastlmm->leap_gwas) (1.15.0) Collecting backports.functools-lru-cache Using cached https://files.pythonhosted.org/packages/da/d1/080d2bb13773803648281a49e3918f65b31b7beebf009887a529357fd44a/backports.functools_lru_cache-1.6.1-py2.py3-none-any.whl Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 Using cached https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl Collecting kiwisolver>=1.0.1 Using cached https://files.pythonhosted.org/packages/3d/78/cb9248b2289ec31e301137cedbe4ca503a74ca87f88cdbfd2f8be52323bf/kiwisolver-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl Collecting h5py>=2.10.0 Using cached https://files.pythonhosted.org/packages/12/90/3216b8f6d69905a320352a9ca6802a8e39fdb1cd93133c3d4163db8d5f19/h5py-2.10.0-cp27-cp27mu-manylinux1_x86_64.whl Collecting bgen-reader>=4.0.4 Using cached https://files.pythonhosted.org/packages/ef/f4/2775ad723b7011603ea1a3ca7021a554465e3175eaa1499590b11960fce7/bgen-reader-4.0.6.tar.gz Installing build dependencies ... error ERROR: Command errored out with exit status 1: command: /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/bin/python /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-x8e5wp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=49.3.0' 'wheel>=0.34.2' cwd: None Complete output (3 lines): DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support ERROR: Could not find a version that satisfies the requirement setuptools>=49.3.0 (from versions: 0.6b1, 0.6b2, 0.6b3, 0.6b4, 0.6rc1, 0.6rc2, 0.6rc3, 0.6rc4, 0.6rc5, 0.6rc6, 0.6rc7, 0.6rc8, 0.6rc9, 0.6rc10, 0.6rc11, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.9.7, 0.9.8, 1.0, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.1.6, 1.1.7, 1.2, 1.3, 1.3.1, 1.3.2, 1.4, 1.4.1, 1.4.2, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.2, 3.0, 3.0.1, 3.0.2, 3.1, 3.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5, 3.5.1, 3.5.2, 3.6, 3.7, 3.7.1, 3.8, 3.8.1, 4.0, 4.0.1, 5.0, 5.0.1, 5.0.2, 5.1, 5.2, 5.3, 5.4, 5.4.1, 5.4.2, 5.5, 5.5.1, 5.6, 5.7, 5.8, 6.0.1, 6.0.2, 6.1, 7.0, 8.0, 8.0.1, 8.0.2, 8.0.3, 8.0.4, 8.1, 8.2, 8.2.1, 8.3, 9.0, 9.0.1, 9.1, 10.0, 10.0.1, 10.1, 10.2, 10.2.1, 11.0, 11.1, 11.2, 11.3, 11.3.1, 12.0, 12.0.1, 12.0.2, 12.0.3, 12.0.4, 12.0.5, 12.1, 12.2, 12.3, 12.4, 13.0.1, 13.0.2, 14.0, 14.1, 14.1.1, 14.2, 14.3, 14.3.1, 15.0, 15.1, 15.2, 16.0, 17.0, 17.1, 17.1.1, 18.0, 18.0.1, 18.1, 18.2, 18.3, 18.3.1, 18.3.2, 18.4, 18.5, 18.6, 18.6.1, 18.7, 18.7.1, 18.8, 18.8.1, 19.0, 19.1, 19.1.1, 19.2, 19.3, 19.4, 19.4.1, 19.5, 19.6, 19.6.1, 19.6.2, 19.7, 20.0, 20.1, 20.1.1, 20.2.2, 20.3, 20.3.1, 20.4, 20.6.6, 20.6.7, 20.6.8, 20.7.0, 20.8.0, 20.8.1, 20.9.0, 20.10.1, 21.0.0, 21.1.0, 21.2.0, 21.2.1, 21.2.2, 22.0.0, 22.0.1, 22.0.2, 22.0.4, 22.0.5, 23.0.0, 23.1.0, 23.2.0, 23.2.1, 24.0.0, 24.0.1, 24.0.2, 24.0.3, 24.1.0, 24.1.1, 24.2.0, 24.2.1, 24.3.0, 24.3.1, 25.0.0, 25.0.1, 25.0.2, 25.1.0, 25.1.1, 25.1.2, 25.1.3, 25.1.4, 25.1.5, 25.1.6, 25.2.0, 25.3.0, 25.4.0, 26.0.0, 26.1.0, 26.1.1, 27.0.0, 27.1.0, 27.1.2, 27.2.0, 27.3.0, 27.3.1, 28.0.0, 28.1.0, 28.2.0, 28.3.0, 28.4.0, 28.5.0, 28.6.0, 28.6.1, 28.7.0, 28.7.1, 28.8.0, 28.8.1, 29.0.0, 29.0.1, 30.0.0, 30.1.0, 30.2.0, 30.2.1, 30.3.0, 30.4.0, 31.0.0, 31.0.1, 32.0.0, 32.1.0, 32.1.1, 32.1.2, 32.1.3, 32.2.0, 32.3.0, 32.3.1, 33.1.0, 33.1.1, 34.0.0, 34.0.1, 34.0.2, 34.0.3, 34.1.0, 34.1.1, 34.2.0, 34.3.0, 34.3.1, 34.3.2, 34.3.3, 34.4.0, 34.4.1, 35.0.0, 35.0.1, 35.0.2, 36.0.1, 36.1.0, 36.1.1, 36.2.0, 36.2.1, 36.2.2, 36.2.3, 36.2.4, 36.2.5, 36.2.6, 36.2.7, 36.3.0, 36.4.0, 36.5.0, 36.6.0, 36.6.1, 36.7.0, 36.7.1, 36.7.2, 36.8.0, 37.0.0, 38.0.0, 38.1.0, 38.2.0, 38.2.1, 38.2.3, 38.2.4, 38.2.5, 38.3.0, 38.4.0, 38.4.1, 38.5.0, 38.5.1, 38.5.2, 38.6.0, 38.6.1, 38.7.0, 39.0.0, 39.0.1, 39.1.0, 39.2.0, 40.0.0, 40.1.0, 40.1.1, 40.2.0, 40.3.0, 40.4.0, 40.4.1, 40.4.2, 40.4.3, 40.5.0, 40.6.0, 40.6.1, 40.6.2, 40.6.3, 40.7.0, 40.7.1, 40.7.2, 40.7.3, 40.8.0, 40.9.0, 41.0.0, 41.0.1, 41.1.0, 41.2.0, 41.3.0, 41.4.0, 41.5.0, 41.5.1, 41.6.0, 42.0.0, 42.0.1, 42.0.2, 43.0.0, 44.0.0, 44.1.0, 44.1.1) ERROR: No matching distribution found for setuptools>=49.3.0 ---------------------------------------- ERROR: Command errored out with exit status 1: /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/bin/python /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-x8e5wp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=49.3.0' 'wheel>=0.34.2' Check the logs for full command output. This is the error message. I have tried to update steuptools to newer version but it does not seem to work. Is it possible to install LEAP using python 3. Thank you — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNCB43S2KI6R2VQCQ4GYLTSHI3X5ANCNFSM4RXLMUTQ> .

[dianacornejo]

Hi, @omerwe
The version of fast-lmm I am using is this one released in january 2020.
Can you please let me know which version of fastlmm did LEAP use to work with? I would like to reproduce the installation you propose in the readme, here is a list of fast-lmm versions
I appreciate your help
Thank you
Diana

[omerwe]

Hi Diana, Thanks for letting me know that FaST-LMM is now under active development again. This is a new development from last year. I haven't maintained LEAP in a long time (several years), but I can try updating it to Python3 and see what happens. Unfortunately I don't have a lot of bandwidth, but I'll try getting around to it sometimes in the next week, fingers crossed. Out of curiosity, do you specifically prefer FaST-LMM+LEAP over one of the newer methods that are out there (e.g. SAIGE) for some reason? Thanks, Omer

…

On Thu, Sep 24, 2020 at 5:36 PM diana.cornejo ***@***.***> wrote: Hi, @omerwe <https://github.com/omerwe> The version of fast-lmm I am using is this one <https://pypi.org/project/fastlmm/0.4.1/> released in january 2020. Can you please let me know which version of fastlmm did LEAP use to work with? I would like to reproduce the installation you propose in the readme, here is a list of fast-lmm versions <https://pypi.org/project/fastlmm/0.4.11/#history> I appreciate your help Thank you Diana — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNCB47HVASXZYCRCJHFH6LSHNKQHANCNFSM4RXLMUTQ> .

[omerwe]

BTW I upgraded the code to Python 3 (and upgraded the readme) but I couldn't install the newest fastlmm package (because there's a problem with the bed-reader installation) so I couldn't test the code. Unfortunately I don't have the bandwidth to look into this any further. Hopefully after bed-reader is fixed I can check if the update works.

…

On Fri, Sep 25, 2020 at 3:54 PM Omer Weissbrod ***@***.***> wrote: Hi Diana, Thanks for letting me know that FaST-LMM is now under active development again. This is a new development from last year. I haven't maintained LEAP in a long time (several years), but I can try updating it to Python3 and see what happens. Unfortunately I don't have a lot of bandwidth, but I'll try getting around to it sometimes in the next week, fingers crossed. Out of curiosity, do you specifically prefer FaST-LMM+LEAP over one of the newer methods that are out there (e.g. SAIGE) for some reason? Thanks, Omer On Thu, Sep 24, 2020 at 5:36 PM diana.cornejo ***@***.***> wrote: > Hi, @omerwe <https://github.com/omerwe> > The version of fast-lmm I am using is this one > <https://pypi.org/project/fastlmm/0.4.1/> released in january 2020. > Can you please let me know which version of fastlmm did LEAP use to work > with? I would like to reproduce the installation you propose in the readme, > here is a list of fast-lmm versions > <https://pypi.org/project/fastlmm/0.4.11/#history> > I appreciate your help > Thank you > Diana > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#6 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/ACNCB47HVASXZYCRCJHFH6LSHNKQHANCNFSM4RXLMUTQ> > . >