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churchill-lab / alntools

Preprocess bam file into a compressed alignment incidence matrix (equivalence class)
https://churchill-lab.github.io/alntools/
MIT License
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Installation issues #14

Open asreedasyam opened 1 month ago

asreedasyam commented 1 month ago

Hello, I'm having trouble installing alntools. I followed the instructions on the GitHub page (https://churchill-lab.github.io/alntools/), but I'm encountering an error when trying to run the tool. Since EMASE installation through conda failed, I skipped it and installed all the other dependencies manually. Running the setup.py script didn't produce any errors, but I get the following error message when I try to use alntools. Any help troubleshooting this installation issue would be greatly appreciated.

Traceback (most recent call last): File "/home/user2/tools/conda_envs/ase/bin/alntools", line 4, in <module> __import__('pkg_resources').run_script('alntools==0.1.1', 'alntools') File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1462, in run_script exec(code, namespace, namespace) File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/EGG-INFO/scripts/alntools", line 11, in <module> from alntools.cli import cli File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/alntools/cli.py", line 9, in <module> from . import bin_utils File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/alntools/bin_utils.py", line 13, in <module> from .matrix.AlignmentPropertyMatrix import AlignmentPropertyMatrix as APM File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/alntools/matrix/AlignmentPropertyMatrix.py", line 3, in <module> import tables File "/home/user2/tools/conda_envs/ase/lib/python2.7/site-packages/tables/__init__.py", line 82, in <module> from tables.utilsextension import ( ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory

mattjvincent commented 1 month ago

Do you have the HDF libraries installed?

asreedasyam commented 1 month ago

Hi Matt, Yes, I have installed h5py. I tried with an older version too h5py=2.6.0 but no luck. Thanks !

mattjvincent commented 1 month ago

I see you are using Conda. Can you install alntools directly from source? I am curious as to where you LD_LIBRARY_PATH is pointing?

export LD_LIBRARY_PATH=[actual location]

Also, what are you trying to do with alntools? Some of the functionality maybe in GBRS (including EMASE).

asreedasyam commented 1 month ago

Ah!! I was trying to use emase-zero for allele-specific expression, but GBRS seems to be the tool I should use. Thanks for the tip.