idr error with narrowPeaks

[wisense]

Hi, I run idr with the test narrowPeaks files and my own narrowPeaks files. They all ended up with an error:

[wszheng@guru idr-2.0.2]$ idr --samples tests/data/peak1 tests/data/peak2 WARNING: Cython does not appear to be installed.- falling back to much slower python method. Initial parameter values: [0.10 1.00 0.20 0.50] /home/wszheng/Install/Python-3.6.1/bin/idr --samples tests/data/peak1 tests/data/peak2 Traceback (most recent call last): File "/home/wszheng/Install/Python-3.6.1/bin/idr", line 4, in import('pkg_resources').run_script('idr==2.0.2', 'idr') File "/home/wszheng/Install/Python-3.6.1/lib/python3.6/site-packages/pkg_resources/init.py", line 654, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/wszheng/Install/Python-3.6.1/lib/python3.6/site-packages/pkg_resources/init.py", line 1434, in run_script exec(code, namespace, namespace) File "/home/wszheng/Install/Source_binaries/idr-2.0.2/idr.egg-info/scripts/idr", line 10, in idr.idr.main() File "/home/wszheng/Install/Source_binaries/idr-2.0.2/idr/idr.py", line 759, in main fix_mu=args.fix_mu, fix_sigma=args.fix_sigma )
File "/home/wszheng/Install/Source_binaries/idr-2.0.2/idr/idr.py", line 391, in fit_model_and_calc_idr fix_mu=fix_mu, fix_sigma=fix_sigma) File "/home/wszheng/Install/Source_binaries/idr-2.0.2/idr/optimization.py", line 468, in estimate_model_params fix_mu=fix_mu, fix_sigma=fix_sigma) File "/home/wszheng/Install/Source_binaries/idr-2.0.2/idr/optimization.py", line 420, in EMP_with_pseudo_value_algorithm z1 = compute_pseudo_values(r1, theta[0], theta[1], theta[3]) File "/home/wszheng/Install/Source_binaries/idr-2.0.2/idr/utility.py", line 46, in py_compute_pseudo_values -10, 10, EPS ) ) TypeError: py_cdf_i() takes 6 positional arguments but 7 were given

Can anyone help me figure out this problem? Thanks very much.

[dcdxy]

@wisense Were you able to find a solution for this? I am experiencing the same issue.

[rcwchan]

Hi,

I received this error and a variety of others (to do with numpy, cython, matplotlib, the error referenced in #34 ) and ultimately got it to work by using the idr provided on bioconda. I created the following conda environment:

conda create --name idr_filtering python=3.6 cython numpy matplotlib scipy libgfortran idr

and it seemed to run after that. Hopefully this is helpful to someone.