Open mtisza1 opened 2 years ago
Adding a note that numpy <1.24.0 is needed, or else BACPHLIP throws an error at the end:
AttributeError: module 'numpy' has no attribute 'float'.
This has got to do with numpy's deprecation of np.float expiring in v1.24.0.
Hi Adam,
Now that I've gotten
BACPHLIP
installed, it's great! Thank you for making this tool.However, I had to struggle for a while to get it working. Based on your listed dependencies, I made a conda environment like this
conda create -n bacphlip -c bioconda biopython pandas joblib scikit-learn hmmer
For whatever reason, conda "solved" this with
biopython 1.70
. I then installedBACPHLIP
with pip. When I ran the tool, I kept getting this biopython error:
AttributeError: 'SeqRecord' object has no attribute 'translate'
I noticed that the version of
biopython
available when you uploaded this package to github was1.77
, so I redid the conda environment as follows, and it works fine.
conda create -n bacphlip python biopython=1.77 pandas joblib scikit-learn hmmer
Because the dependency versions can matter quite a bit, I'm wondering if you can post the versions of each package that worked for you. This should help people install your tool.
Best,
Mike
Thanks for sharing, followed your steps and it has been successfully installed.
Hi Adam,
Now that I've gotten
BACPHLIP
installed, it's great! Thank you for making this tool.However, I had to struggle for a while to get it working. Based on your listed dependencies, I made a conda environment like this
conda create -n bacphlip -c bioconda biopython pandas joblib scikit-learn hmmer
For whatever reason, conda "solved" this with
biopython 1.70
. I then installedBACPHLIP
with pip. When I ran the tool, I kept getting this biopython error:
AttributeError: 'SeqRecord' object has no attribute 'translate'
I noticed that the version of
biopython
available when you uploaded this package to github was1.77
, so I redid the conda environment as follows, and it works fine.
conda create -n bacphlip python biopython=1.77 pandas joblib scikit-learn hmmer
Because the dependency versions can matter quite a bit, I'm wondering if you can post the versions of each package that worked for you. This should help people install your tool.
Best,
Mike
Thank you, this also worked for me but I had to install python 3.8, the 3.9 was creating issues with numpy.
Cheers,
Johan Sebastián
AttributeError: module 'numpy' has no attribute 'float'.
You're right, I downgraded the version before it worked.
conda activate bacphlip
conda install -c conda-forge -c bioconda numpy=1.23.5
Hi Adam,
Now that I've gotten
BACPHLIP
installed, it's great! Thank you for making this tool.However, I had to struggle for a while to get it working. Based on your listed dependencies, I made a conda environment like this
conda create -n bacphlip -c bioconda biopython pandas joblib scikit-learn hmmer
For whatever reason, conda "solved" this with
biopython 1.70
. I then installedBACPHLIP
with pip. When I ran the tool, I kept getting this biopython error:AttributeError: 'SeqRecord' object has no attribute 'translate'
I noticed that the version of
biopython
available when you uploaded this package to github was1.77
, so I redid the conda environment as follows, and it works fine.conda create -n bacphlip python biopython=1.77 pandas joblib scikit-learn hmmer
Because the dependency versions can matter quite a bit, I'm wondering if you can post the versions of each package that worked for you. This should help people install your tool.
Best,
Mike