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ResolutionError: Script 'scripts/ragtag.py' not found in metadata

See original GitHub issue

I am running the command

 python3 ragtag_scaffold.py /home/mariano/Documents/Wellinger/GCA_002057635.1_ASM205763v1_genomic.fna /home/mariano/Documents/Wellinger/GCA_000773925.1_ASM77392v1_genomic.fna-1 --aligner /home/mariano/Downloads/minimap2/minimap2

and I get this error in the file ragtag.scaffold.err:

Traceback (most recent call last):
  File "/home/mariano/miniconda3/bin/ragtag_agp2fa.py", line 4, in <module>
    __import__('pkg_resources').run_script('RagTag==2.0.1', 'ragtag_agp2fa.py')
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 650, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1434, in run_script
    raise ResolutionError(
pkg_resources.ResolutionError: Script 'scripts/ragtag_agp2fa.py' not found in metadata at '/home/mariano/miniconda3/lib/python3.8/site-packages/RagTag-2.0.1.dist-info'

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:6 (2 by maintainers)

github_iconTop GitHub Comments

1reaction
mavinocommented, Sep 29, 2021

It looks I fixed the problem with the following

conda create -n ragtag python=3.7.3
conda activate ragtag
conda install -c bioconda ragtag
ragtag.py

RagTag: Tools for fast and flexible genome assembly scaffolding and improvement.
Version: v2.0.1

usage: ragtag.py <command> [options]
    
    assembly improvement:
      correct         homology-based misassembly correction
      scaffold        homology-based assembly scaffolding
      patch           homology-based assembly patching
      merge           scaffold merging
      
    file utilities:
      agp2fa          build a FASTA file from an AGP file
      agpcheck        check for valid AGP file format
      asmstats        assembly statistics
      splitasm        split an assembly at gaps
      delta2paf       delta to PAF file conversion
      paf2delta       PAF to delta file conversion
      updategff       update gff intervals
      

    options:
      -c, --citation  
      -v, --version
0reactions
mavinocommented, Sep 29, 2021

Searching for “failed with initial frozen solve. Retrying with flexible solv” which I always get when I use conda I came across https://stackoverflow.com/questions/57518050/conda-install-and-update-do-not-work-also-solving-environment-get-errors and I used some of their solutions:

conda update --all --yes

After that I retried:

conda install -c bioconda ragtag
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                                      

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.27=0
  - python=3.8 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.27
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