install LAT error #176
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I was able to solve this by using python 3.6. Just copy the last bit of code from .travis/install.sh conda create -q -n test-environment python=3.6 numpy scipy matplotlib sphinx tabulate |
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Hello! I either |
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Hi Pavel,
Does your cluster run CentOS? If so, you might have different Python
modules for different versions. You can check by running module avail, and
then activate by running module load Python3.7 or something.
This might solve the problem if the Python version is indeed causing the
problem. Let me know if it doesn't work.
Michael
…On Thu, Dec 5, 2024, 03:59 Pavel Tomanek ***@***.***> wrote:
Hello!
I am trying to install KAT on HPC cluster in UGent, we have EasyBuild for
building/installing software.
I have Python 3.11.3, but the installation crash on configure step with:
checking for python3... /apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python3
configure: Found python version: 3.11.3
checking for a version of Python >= '3.1.0'... yes
checking for a version of Python >= '3.5'... no
configure: WARNING: this package requires Python >= '3.5'.
If you have it installed, but it isn't the default Python
interpreter in your system path, please pass the PYTHON_VERSION
variable to configure. See ``configure --help'' for reference.
configure: Environment variable 'PYTHON_VERSION' set to:
checking for the distutils Python package... yes
checking for Python include path... -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11
checking for Python library path... -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/lib -lpython3.11
checking for Python site-packages path... /apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/site-packages
checking python extra libraries... -ldl -lm -lpthread -lutil -lm
checking python extra linking flags... -Xlinker -export-dynamic
checking consistency of all components of python development environment... yes
configure: error:
Python3 not detected.
We suggest installing python3 via conda with the required packages (numpy, scipy, matplotlib, sphinx).
Please see .travis/install.sh for details of how we do this.
Alternatively, try installing python anaconda.
I either export PYTHON_VERSION=3.11 but the error is still the same.
I can not use conda/anaconda, just pip.
Could you help me with this, please?
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Hello @DeadlineWasYesterday! EDIT: |
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Hi Pavel,
You could try something like Docker or Singularity to have more control
over the environment.
You could also try user installing Python from source. If the environment
is too restricted, it might still not work. If so, you'll need to modify
the PATH variable and check if which python and which python3 are detecting
the right version.
It might also be easier to run on a user workstation without these issues,
or revert to another kmer analysis software.
…On Thu, Dec 5, 2024, 06:12 Pavel Tomanek ***@***.***> wrote:
Hello @DeadlineWasYesterday <https://github.com/DeadlineWasYesterday>!
Our clusters have RHEL 8 or 9. The python version is linked to toolchain
version and for now I can use Python 3.11.3 and later (3.11.5, 3.12.3) not
older .
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The version of Python installed on the system is 3.10.12
Error:
checking for python3... /usr/local/bin/python3
configure: Found python version: 3.10.12
checking for a version of Python >= '3.1.0'... yes
checking for a version of Python >= '3.5'... no
configure: WARNING: this package requires Python >= '3.5'.
If you have it installed, but it isn't the default Python
interpreter in your system path, please pass the PYTHON_VERSION
variable to configure. See ``configure --help'' for reference.
configure: Environment variable 'PYTHON_VERSION' set to:
checking for the distutils Python package... yes
checking for Python include path... -I/usr/local/include/python3.10
checking for Python library path... -L/usr/local/lib -lpython3.10
checking for Python site-packages path... /usr/local/lib/python3.10/site-packages
checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm
checking python extra linking flags... -Xlinker -export-dynamic
checking consistency of all components of python development environment... yes
configure: error:
Python3 not detected.
We suggest installing python3 via conda with the required packages (numpy, scipy, matplotlib, sphinx).
Please see .travis/install.sh for details of how we do this.
Alternatively, try installing python anaconda.
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