Install IRIS error

[mguaita]

Hello,

We are trying to install IRIS in our research cluster and we get this error.

CondaFileIOError: 'conda_requirements_py2.txt'. [Errno 2] No such file or directory: 'conda_requirements_py2.txt'

Also, is it possible to run IRIS on Python 3? As there is a: 'conda_requirements_py3.txt'

This is the terminal installing output:

[root@afrodita-login IRIS]# ./install core

checking conda
WARNING: A conda environment already exists at '/root/conda_env_2'
Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /root/conda_env_2

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate /root/conda_env_2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

WARNING: A conda environment already exists at '/root/conda_env_3'
Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /root/conda_env_3

Proceed ([y]/n)? y 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate /root/conda_env_3
#
# To deactivate an active environment, use
#
#     $ conda deactivate

WARNING: A conda environment already exists at '/root/conda_env_samtools'
Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /root/conda_env_samtools

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

#
# To activate this environment, use
#
#     $ conda activate /root/conda_env_samtools
#
# To deactivate an active environment, use
#
#     $ conda deactivate

checking python dependencies

CondaFileIOError: 'conda_requirements_py2.txt'. [Errno 2] No such file or directory: 'conda_requirements_py2.txt'

[root@afrodita-login IRIS]# nano conda_requirements_py2.txt

[root@afrodita-login IRIS]# nano conda_requirements_py2.txt

[root@afrodita-login IRIS]# ./install core

checking conda

WARNING: A conda environment already exists at '/root/conda_env_2'

Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done

Solving environment: done

## Package Plan ##
  environment location: /root/conda_env_2

Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

#
# To activate this environment, use
#
#     $ conda activate /root/conda_env_2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

WARNING: A conda environment already exists at '/root/conda_env_3'

Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done

Solving environment: done

## Package Plan ##

  environment location: /root/conda_env_3

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

#
# To activate this environment, use
#
#     $ conda activate /root/conda_env_3
#
# To deactivate an active environment, use
#
#     $ conda deactivate

WARNING: A conda environment already exists at '/root/conda_env_samtools'

Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /root/conda_env_samtools

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

#
# To activate this environment, use
#
#     $ conda activate /root/conda_env_samtools
#
# To deactivate an active environment, use
#
#     $ conda deactivate

checking python dependencies

CondaFileIOError: 'conda_requirements_py2.txt'. [Errno 2] No such file or directory:  'conda_requirements_py2.txt'

[root@afrodita-login IRIS]# cat conda_requirements_py2.txt
bedtools=2.29.0
numpy=1.16.5
pybigwig=0.3.13
python=2.7.*
scipy=1.2.0
seaborn=0.9.0
statsmodels=0.10.2

[EricKutschera]

It is not possible to run IRIS with Python 3. The file conda_requirements_py3.txt is for installing the snakemake workflow manager which will run the IRIS code using Python 2

From the output you posted it looks like the ./install command was run in a directory named IRIS (based on the command prompt), but somehow the conda commands were run in /root/. My guess is that set_env_vars.sh is not behaving as expected at this line: https://github.com/Xinglab/IRIS/blob/v2.0.1/set_env_vars.sh#L8

It's trying to find the directory of the script, but it seems like it's finding /root/ instead of the IRIS/ directory. You could edit that file to directly set SCRIPT_DIR='/path/to/IRIS/'

[mguaita]

Hello Eric,

Your guess was right, we have been able to complete the installation of IRIS running ./install all.

We have another question that is whether is possible to run individual functions of IRIS without the Snakemake file and how? The command IRIS -h or _IRIS function -h_ does not seem to work. The command ./run for the example test does work though.

Thank you very much!

[EricKutschera]

You can run individual IRIS commands when you have the conda environment activated

conda activate ./conda_env_2
IRIS -h

The ./run script works by activating conda environments as needed

[mguaita]

Thank you very much Eric!