Hello,
Can you please install Locator on the cluster system?
Available as a conda here: GitHub - kr-colab/locator: deep learning prediction of geographic location from individual genome sequences
Many thanks!
When trying to install it myself, following the procedure, I receive the below error (after creating the cond environment and cloning the git). I'm new to conda environments and unsure of the origin of this error.
Many Thanks
pip install -r req.txt
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
Collecting numpy (from -r req.txt (line 1))
Downloading https://files.pythonhosted.org/packages/3a/5f/47e578b3ae79e2624e205445ab77a1848acdaa2929a00eeef6b16eaaeb20/numpy-1.16.6-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB)
|████████████████████████████████| 17.0MB 25.4MB/s
Collecting tensorflow (from -r req.txt (line 2))
Downloading https://files.pythonhosted.org/packages/ef/73/205b5e7f8fe086ffe4165d984acb2c49fa3086f330f03099378753982d2e/tensorflow-2.1.0-cp27-cp27mu-manylinux2010_x86_64.whl (421.8MB)
|████████████████████████████████| 421.8MB 42kB/s
Collecting h5py (from -r req.txt (line 3))
Downloading https://files.pythonhosted.org/packages/12/90/3216b8f6d69905a320352a9ca6802a8e39fdb1cd93133c3d4163db8d5f19/h5py-2.10.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
|████████████████████████████████| 2.8MB 50.6MB/s
Collecting scikit-allel (from -r req.txt (line 4))
Downloading https://files.pythonhosted.org/packages/13/5f/4a45c9d788cf74eb5a6536ceab78ff72806ac36dfed07abb54fc72f9a39f/scikit-allel-1.3.5.tar.gz (9.7MB)
|████████████████████████████████| 9.7MB 48.4MB/s
Installing build dependencies ... error
ERROR: Command errored out with exit status 1:
command: /bin/python /usr/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-AHUEAz/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=45' wheel 'Cython>=0.28.5' 'setuptools_scm[toml]>=6.0' oldest-supported-numpy
cwd: None
Complete output (6 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
Collecting setuptools>=45
ERROR: Could not find a version that satisfies the requirement setuptools>=45 (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>=45
WARNING: You are using pip version 19.2.1, however version 20.3.4 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
----------------------------------------
ERROR: Command errored out with exit status 1: /bin/python /usr/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-AHUEAz/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=45' wheel 'Cython>=0.28.5' 'setuptools_scm[toml]>=6.0' oldest-supported-numpy Check the logs for full command output.
WARNING: You are using pip version 19.2.1, however version 20.3.4 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Hello,
It seems related to python2 (Setuptools 45 declares its supported Python versions to exclude Python 2.7, and installers such as pip 9 or later will honor this declaration and prevent installation of Setuptools 45 or later in Python 2 environments).
I tried with python3 and --user option
pip3 install --user -r req.txt
But now it fails, asking for python3-devel package 
Could not find <Python.h>. This could mean the following:
* You're on Ubuntu and haven't run `apt-get install python3-dev`.
* You're on RHEL/Fedora and haven't run `yum install python3-devel` or
`dnf install python3-devel` (make sure you also have redhat-rpm-config
installed)
* You're on Mac OS X and the usual Python framework was somehow corrupted
(check your environment variables or try re-installing?)
* You're on Windows and your Python installation was somehow corrupted
(check your environment variables or try re-installing?)
@team.software any tricks ?
Hi, thanks for giving it a try! Is there any updates on this?
Mon protocole :
module load python/3.9
python -m venv venv_locator
. venv_locator/bin/activate
git clone https://github.com/kr-colab/locator.git
cd locator/
pip install -r req.txt
python setup.py install
Mais
Installed /shared/ifbstor1/home/glecorguille/tmp/venv_locator/lib/python3.9/site-packages/gnuplotlib-0.38-py3.9.egg
Searching for scipy==1.4.1
Reading https://pypi.org/simple/scipy/
Downloading https://files.pythonhosted.org/packages/04/ab/e2eb3e3f90b9363040a3d885ccc5c79fe20c5b8a3caa8fe3bf47ff653260/scipy-1.4.1.tar.gz#sha256=dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59
Best match: scipy 1.4.1
Processing scipy-1.4.1.tar.gz
Writing /tmp/easy_install-u46vk89v/scipy-1.4.1/setup.cfg
Running scipy-1.4.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-u46vk89v/scipy-1.4.1/egg-dist-tmp-d6qqfkwu
/tmp/easy_install-u46vk89v/scipy-1.4.1/setup.py:418: UserWarning: Unrecognized setuptools command ('-q bdist_egg --dist-dir /tmp/easy_install-u46vk89v/scipy-1.4.1/egg-dist-tmp-d6qqfkwu'), proceeding with generating Cython sources and expanding templates
warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
Running from scipy source directory.
/shared/ifbstor1/home/glecorguille/tmp/venv_locator/lib/python3.9/site-packages/numpy/distutils/system_info.py:1902: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
/shared/ifbstor1/home/glecorguille/tmp/venv_locator/lib/python3.9/site-packages/numpy/distutils/system_info.py:1902: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
/shared/ifbstor1/home/glecorguille/tmp/venv_locator/lib/python3.9/site-packages/setuptools/sandbox.py:140: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
type, exc = map(pickle.loads, self._saved)
error: No lapack/blas resources found.
Je ne pense pas avoir plus de temps aujourd'hui pour m'y plonger.
Peut-être partir d'un env conda "perso" avec Lapack :: Anaconda.org ?