I have installed some ucsc tools on my Mac computer and it worked fine: ### Installation conda create --name ucsc-netchainsubset377 --channel bioconda --yes ucsc-netchainsubset=377 ### Conda environment activation source activate ucsc-netchainsubset377 ### Checking the tool's help netchainsubset netChainSubset - Create chain file with subset of chains that appear in the net usage: netChainSubset in.net in.chain out.chain options: -gapOut=gap.tab - Output gap sizes to file -type=XXX - Restrict output to particular type in net file -splitOnInsert - Split chain when get an insertion of another chain -wholeChains - Write entire chain references by net, don't split when a high-level net is encoundered. This is useful when nets have been filtered. -skipMissing - skip chains that are not found instead of generating an error. Useful if chains have been filtered. The same commands on GNU/Linux produced the following error: netchainsubset netchainsubset: command not found even though the tool seems to be installed successfully: Downloading and Extracting Packages ucsc-netchainsubset- | 310 KB | ############################################################################ | 100% mysql-connector-c-6. | 4.4 MB | ############################################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done The same happened with `ucsc-fatotwobit` and `ucsc-liftup` and I would not be surprised if this behaviour affected the whole suite of ucsc programmes installed through conda. Anyone can suggest a solution? Cheers.