provide support for conda

[kmnip]

• add requirements file for conda environment
• update readme, usage, and installation
• remove unused option in tap2.py
• update parameters for RNA-Bloom

[readmanchiu]

Ka Ming, I have problem creating the conda enviornment: First, I tried mamba. I only have mamba installed within a conda environment. So either within the conda environment, or outside of it using the full path of mamba, I couldn't run mamba activate. It said I need to run mamba init to activate/deactivate, I did not but I still couldn't activate the environment.

Then I tried conda. But it gave me this message after I tried conda install:

(/projects/btl/rchiu/pavfinder) [rchiu@gphost02 pavfinder]$ conda install -f conda_requirements.txt -c conda-forge -c bioconda

WARNING: The --force flag will be removed in a future conda release.
         See 'conda install --help' for details about the --force-reinstall
         and --clobber flags.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - conda_requirements.txt

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/r/linux-64
  - https://conda.anaconda.org/r/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://conda.anaconda.org/dranew/linux-64
  - https://conda.anaconda.org/dranew/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

[readmanchiu]

oh, I figured out...have to use --file instead of -f. Maybe it's the version of conda, mine is 4.10.1.

[kmnip]

Thanks for catching that. I have update the commands.

[readmanchiu]

How do I locate the scripts? I would recommend putting the scripts like fusion-bloom, tap.py, tap2.py, pavfinder, extract_transcript_sequence.py in the bin directory

[kmnip]

Right now, I am just setting up the conda environment to run the scripts. How the scripts are run is still exactly the same as how it used to be.

After this is done, we will need to make a release for these changes. Then, we can make a recipe in bioconda.

[readmanchiu]

ok, then I would run the script through the git repo locations. setup.py put all the scripts in the bin of the local environment. If you install through pip with the github path, all the scripts can be invoked without specifying the path. I think this is desirable to have in the conda environment if there is a way to do it. I guess conda didn't look at setup.py when setting up the environment

[kmnip]

In that case, I think we need to add some instructions for setting up the PATH and PYTHONPATH

[readmanchiu]

hmmm...how would you run pavfinder after setting up the conda environment then, doesn't seem to work

[kmnip]

Added instructions in INSTALL.md for setting up PATH and PYTHONPATH