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Uninstalling

An installation is removed whole: its conda environment, its analysis environment where one is installed, the pipeline under ~/.local/opt, and the links in ~/.local/bin. Versions are separate, so removing one leaves the others working. PoolSeqFlow list shows what is on the machine.

One version

PoolSeqFlow uninstall            # the only installation, or it asks which
PoolSeqFlow-3.1.1 uninstall      # that version, named
  • With several versions installed, plain PoolSeqFlow uninstall lists them and asks which. In a script, where there is nothing attached to ask, it refuses rather than guessing; name the version instead.
  • Plain PoolSeqFlow is re-pointed at the newest version that remains, and removed once none does.
  • PoolSeqFlow analysis uninstall removes only that release's analysis environment, leaving the pipeline installed.
  • If you installed with POOLSEQFLOW_PREFIX set, set it again: an uninstall looks only under that prefix.

Every version

PoolSeqFlow uninstall all

Every PoolSeqFlow conda environment on the machine, every installed pipeline, and the links in bin.

What is not touched

  • Your projects. parameters.config, Data/, Reference/ and everything in storageDir sit outside every installation, including the analyses a module has already produced.
  • Another version's modules. A module store belongs to the installation that holds it, so modules go with that version and with no other.

Both forms list what will go and ask before anything does. The tab completions go with the last version removed; another version left installed keeps them.

Removing an environment means results produced with that version can no longer be reproduced without reinstalling it.

On a network filesystem the directory can outlive its contents. Files the running command still has open leave .nfs* placeholders behind, so the pipeline directory cannot remove itself from under itself. It says so, and prints the one rm -rf that finishes the job after the command has exited.