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YangLab / CLEAR

direct comparison of circular and linear RNA expression
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Installation issue #1

Closed jpessin-BU closed 4 years ago

jpessin-BU commented 4 years ago

When installing as per instructions, the installer runs without error, however, there seem to be some underlying linking/module placing and finding issues. (I've had the same issue with multiple python3 installations, for reproducibly here it is in conda on Linux)

conda activate clear
conda install circexplorer2 -c bioconda
git clone https://github.com/YangLab/CLEAR.git
cd CLEAR
python ./setup.py install

. . . verbose checking creating copying . . . 

Adding CLEAR 1.0.0 to easy-install.pth file
Installing circ_quant script to /usr2/collab/pessinj/.conda/envs/clear/bin
Installing clear_quant script to /usr2/collab/pessinj/.conda/envs/clear/bin
Installed /usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/CLEAR-1.0.0-py3.6.egg
Processing dependencies for CLEAR==1.0.0
Searching for pybedtools==0.8.0
Best match: pybedtools 0.8.0
Adding pybedtools 0.8.0 to easy-install.pth file
Using /usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages
Searching for pysam==0.15.3
Best match: pysam 0.15.3 
Adding pysam 0.15.3 to easy-install.pth file
Using /usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages 
Searching for six==1.12.0
Best match: six 1.12.0
Adding six 1.12.0 to easy-install.pth file
Using /usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages
Finished processing dependencies for CLEAR==1.0.0

clear_quant and circ_quant are now in the path

(clear) [pessinj@scc2 clear]$ which clear_quant
~/.conda/envs/clear/bin/clear_quant 
(clear) [pessinj@scc2 clear]$ which circ_quant
~/.conda/envs/clear/bin/circ_quant

But clear_quant cannot find circ_quant

(clear) [pessinj@scc2 CLEAR]$ clear_quant -h Traceback (most recent call last): File "/usr2/collab/pessinj/.conda/envs/clear/bin/clear_quant", line 11, in load_entry_point('CLEAR==1.0.0', 'console_scripts', 'clear_quant')() File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 2843, in load_entry_point return ep.load() File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 2434, in load return self.resolve() File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 2440, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/CLEAR-1.0.0-py3.6.egg/src/run .py", line 11, in ModuleNotFoundError: No module named 'circ_quant'

and circ_quant cannot find spReads

(clear) [pessinj@scc2 CLEAR]$ circ_quant -h Traceback (most recent call last): File "/usr2/collab/pessinj/.conda/envs/clear/bin/circ_quant", line 11, in load_entry_point('CLEAR==1.0.0', 'console_scripts', 'circ_quant')() File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 2843, in load_entry_point return ep.load() File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 2434, in load return self.resolve() File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/pkg_resources/__init__.py", l ine 2440, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/usr2/collab/pessinj/.conda/envs/clear/lib/python3.6/site-packages/CLEAR-1.0.0-py3.6.egg/src/cir c_quant.py", line 19, in ModuleNotFoundError: No module named 'spReads'

spReads is in the git repo 

(clear) [pessinj@scc2 CLEAR]$ find $PWD -name spRead* 
/usr2/collab/pessinj/CLEAR/build/lib/src/spReads.py 
/usr2/collab/pessinj/CLEAR/src/spReads.py

but some quick use of find does not turn it up in the conda-python space

(clear) [pessinj@scc2 CLEAR]$ cd ~/.conda/envs/clear/
(clear) [pessinj@scc2 clear]$ find $PWD -name spRead*
(clear) [pessinj@scc2 clear]$ find $PWD -name clear*
/usr2/collab/pessinj/.conda/envs/clear
/usr2/collab/pessinj/.conda/envs/clear/bin/clear
/usr2/collab/pessinj/.conda/envs/clear/bin/clear_quant
(clear) [pessinj@scc2 clear]$ find $PWD -name circ*
/usr2/collab/pessinj/.conda/envs/clear/bin/circ_quant
/usr2/collab/pessinj/.conda/envs/clear/conda-meta/circexplorer2-2.3.6-py_0.json
shameem356 commented 4 years ago

I am also facing same issue. could you please look into the issue.