Problem with bedtools merge when calling peaks

[CrystalShann]

Hi,

I was running Clippy in a Python environment and consistently encountered issues when calling peaks using bedtools, although calling summits worked as expected. I believe the problem stems from pybedtools not functioning correctly—likely due to version incompatibility with Clippy. I ran into the same issue when attempting to install Clippy via Conda; even when using the libmamba solver, bedtools=2.26.0 could not be resolved. This suggests that Clippy may depend on outdated packages that are no longer compatible with standard installation methods.

error when trying to call peaks in python environment

Command was:
	bedtools merge -s -o sum,distinct -i /tmp/pybedtools.gyhtk4co.tmp -c 11,6
Error message was:
*****
***** ERROR: Requested column 11, but database file /tmp/pybedtools.gyhtk4co.tmp only has fields 1 - 0.

error when trying to install clippy

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides bedtools 2.26.0.* needed by clippy-1.3.1-pyhdfd78af_0

Could not solve for environment specs
The following package could not be installed
└─ clippy is not installable because it requires
   └─ bedtools 2.26.0.* , which does not exist (perhaps a missing channel).