Potential solution for clipper installation

[jechia]

I tried to install the clipper with conda several times.
First several tries all output weird usage from peaksmodule.cc.
I asked for help from chatGPT and I figured out that it was the error with line 512 in peaksmodule.cc,
change the line "PyModule_Create(&peaksmodule);" into "return PyModule_Create(&peaksmodule);".
Then the program work properly for me.

[haibol2016]

Here is my way to install clipper in a linux platform using micromamba

cd clipper
 perl -p -e 's{(.+?=[^=]+).+}{$1}' environment3.yml  > environment3.2.yml 
 micromamba create -f environment3.2.yml --channel-priority flexible
pip install .

However after installation, I found that the wierd options:

clipper -h

Usage`is ? [options]
file_in is a file with a list of the length of aligned reads (only the part that aligns) ``
Options
-L Effective Gene Length
-r # of iterations
-f input file containing read lengths
-a B-H FDR cutoff, default(.05) ... gets very slow as alpha gets smaller
-T 1/0 default(0) print running time statistics
Output:
Significance Threshold [tab] Iterations with this observed threshold

[xiatianjihao]

I have the same problem when I installed the clipper.

Usage`is ? [options]
file_in is a file with a list of the length of aligned reads (only the part that aligns) ``
Options
-L Effective Gene Length
-r # of iterations
-f input file containing read lengths
-a B-H FDR cutoff, default(.05) ... gets very slow as alpha gets smaller
-T 1/0 default(0) print running time statistics
Output:
Significance Threshold [tab] Iterations with this observed threshold