Install Broken on M2 Mac

[josephdviviano]

Hello, I'm unable to install this tool. Please advise.

(anarci) jdv@delarge ~/code/ANARCI:
pip install .
Processing /Users/jdv/code/ANARCI
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: anarci
  Building wheel for anarci (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [613 lines of output]
      /Users/jdv/miniconda3/envs/anarci/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
      !!

              ********************************************************************************
              Please avoid running ``setup.py`` directly.
              Instead, use pypa/build, pypa/installer or other
              standards-based tools.

              See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
              ********************************************************************************

      !!
        self.initialize_options()
      INFO: ANARCI lives in:  /Users/jdv/miniconda3/envs/anarci/lib/python3.10/site-packages/anarci
      INFO: Downloading germlines from IMGT and building HMMs...
      INFO: running 'RUN_pipeline.sh', this will take a couple a minutes.
      Parsed and saved Homo+sapiens HV
      Parsed and saved Mus HV
      Parsed and saved Rattus+norvegicus HV
      Parsed and saved Oryctolagus+cuniculus HV
      Parsed and saved Macaca+mulatta HV
      Parsed and saved Sus+scrofa HV
      Parsed and saved Vicugna+pacos HV
      Parsed and saved Bos+taurus HV
      Parsed and saved Homo+sapiens HJ
      Parsed and saved Mus HJ
      Parsed and saved Rattus+norvegicus HJ
      Parsed and saved Oryctolagus+cuniculus HJ
      Parsed and saved Macaca+mulatta HJ
      Parsed and saved Sus+scrofa HJ
      Parsed and saved Vicugna+pacos HJ
      Parsed and saved Bos+taurus HJ
      Parsed and saved Homo+sapiens KV
      Parsed and saved Mus KV
      Parsed and saved Rattus+norvegicus KV
      Parsed and saved Oryctolagus+cuniculus KV
      Parsed and saved Macaca+mulatta KV
      Parsed and saved Sus+scrofa KV
      Parsed and saved Bos+taurus KV
      Parsed and saved Homo+sapiens KJ
      Parsed and saved Mus KJ
      Parsed and saved Rattus+norvegicus KJ
      Parsed and saved Oryctolagus+cuniculus KJ
      Parsed and saved Macaca+mulatta KJ
      Parsed and saved Sus+scrofa KJ
      Parsed and saved Bos+taurus KJ
      Parsed and saved Homo+sapiens LV
      Parsed and saved Mus LV
      Parsed and saved Rattus+norvegicus LV
      Parsed and saved Oryctolagus+cuniculus LV
      Parsed and saved Macaca+mulatta LV
      Parsed and saved Sus+scrofa LV
      Parsed and saved Bos+taurus LV
      Parsed and saved Homo+sapiens LJ
      Parsed and saved Mus LJ
      Parsed and saved Rattus+norvegicus LJ
      Parsed and saved Oryctolagus+cuniculus LJ
      Parsed and saved Macaca+mulatta LJ
      Parsed and saved Sus+scrofa LJ
      Parsed and saved Bos+taurus LJ
      Parsed and saved Homo+sapiens AV
      Parsed and saved Mus AV
      Parsed and saved Homo+sapiens AJ
      Parsed and saved Mus AJ
      Parsed and saved Homo+sapiens BV
      Parsed and saved Mus BV
      Parsed and saved Homo+sapiens BJ
      Parsed and saved Mus BJ
      Parsed and saved Homo+sapiens GV
      Parsed and saved Mus GV
      Parsed and saved Homo+sapiens GJ
      Parsed and saved Mus GJ
      Parsed and saved Homo+sapiens DV
      Parsed and saved Mus DV
      Parsed and saved Homo+sapiens DJ
      Parsed and saved Mus DJ

      Formatting alignments

      IGs
      Homo_sapiens H
      Homo_sapiens K
      Homo_sapiens L
      Mus H
      Mus K
      Mus L
      Rattus_norvegicus H
      Rattus_norvegicus K
      Rattus_norvegicus L
      Oryctolagus_cuniculus H
      Oryctolagus_cuniculus K
      Oryctolagus_cuniculus L
      Macaca_mulatta H
      Macaca_mulatta K
      Macaca_mulatta L
      Sus_scrofa H
      Sus_scrofa K
      Sus_scrofa L
      Vicugna_pacos H
      Bos_taurus H
      Bos_taurus K
      Bos_taurus L

      TRs
      Homo_sapiens A
      Homo_sapiens B
      Homo_sapiens G
      Homo_sapiens D
      Mus A
      Mus B
      Mus G
      Mus D

      Warning - this alignment doesn't feature CYS at position 23 and/or position 104.
      EIVLTQS.PAVLSMAPKERVTITCQASQNI......NKWLAWYHQEPGRAPKLLIYEA.......SKLITGVP.SRFSGSG..SGTDFTLTISSLEPEDAGTYYCLQS,('Mus', 'K'),('Mustela putorius furo_JIRA1106', 'IGKV1-63*01')
      Warning - this alignment doesn't feature CYS at position 23 and/or position 104.
...
      EIVLTQSPAFRSVTLKEKVT.ITCQASQSI......GSSLHWYQQKPDQSPKLLIKYA.......SQSISGVP.SRFSGSG..SGTDFTLTINSLEAEDAATYYCQQS,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV6-55*01')
      Traceback (most recent call last):
        File "/Users/jdv/code/ANARCI/build_pipeline/./FormatAlignments.py", line 480, in <module>
          main()
        File "/Users/jdv/code/ANARCI/build_pipeline/./FormatAlignments.py", line 454, in main
          jalignments = format_j_genes(jalignments)
        File "/Users/jdv/code/ANARCI/build_pipeline/./FormatAlignments.py", line 179, in format_j_genes
          pr = Popen( [ "muscle_macOS", "-in", ffile, "-gapopen", "-10", "-out", al_filename, ], stdout=PIPE, stderr=PIPE )
        File "/Users/jdv/miniconda3/envs/anarci/lib/python3.10/subprocess.py", line 971, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/Users/jdv/miniconda3/envs/anarci/lib/python3.10/subprocess.py", line 1863, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      FileNotFoundError: [Errno 2] No such file or directory: 'muscle_macOS'
      Alignment input open failed.
         couldn't open ./curated_alignments/ALL.stockholm for reading

      Error: File existence/permissions problem in trying to open HMM file ./HMMs/ALL.hmm.
      HMM file ./HMMs/ALL.hmm not found (nor an .h3m binary of it)

      error: [Errno 2] No such file or directory: 'curated_alignments/germlines.py'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for anarci
  Running setup.py clean for anarci
Failed to build anarci
ERROR: Could not build wheels for anarci, which is required to install pyproject.toml-based projects

[eElor]

Got same error using pyenv (Linux).

@josephdviviano, you can refer to issue #31.

In my case I installed muscle with my package manager (sudo apt install muscle; in your case you could use brew) and updated the path as described in the last comment in #31 (build_pipeline/FormatAlignments.py:181; in your case build_pipeline/FormatAlignments.py:179) with the path of the new muscle installation (sh: echo $(which muscle)).

Currently, I'm just testing anarci locally. But bug (? -> already mentioned in several issues; @broncio123) could make deployment pipeline of apps using anarci as dependency more complicated than necessary. Instead of installing it with a deployment script, like pip install git+https://github.com/oxpig/ANARCI, one would need to clone the repo manually, inspect the target system / container image, update named path, and copy again the cloned and updated repo into the target image.

[eElor]

This bug is weird, since this repo includes a copy of muscle (bin/muscle and bin/muscle_macOS), and after installing anarci (modification above required), which muscle now points my pyenv dir (${HOME}/.pyenv/shims/muscle), which should have derived from the copy of muscle in this repo. Why is bin/muscle not correctly used from the beginning in setup.py? Using the new copy in shims seems to work correctly.

[eElor]

Referencing the path to the muscle binary included in the repo in build_pipeline/FormatAlignments.py:181 lead to initial error.

[eElor]

@broncio123 , I did further installation tests on my system by deleting and recreating my virtual environment. IMHO, muscle could be listed as a requirement for the installation of anarci as currently are hmmer and biopython.

I left build_pipeline/FormatAlignments.py:181 as it initially was, but deleted the muscle binaries included in bin/ and updated setup.py:49 to data_files = [ ('bin', ['bin/ANARCI']) ],. Now, the installation of muscle in my system is correctly recognized during setup and I can install anarci without errors.

Steps (Linux):

sudo apt install hmmer muscle 

git clone https://github.com/oxpig/ANARCI.git anarci
cd anarci
# update `setup.py:49` -> `data_files = [ ('bin', ['bin/ANARCI']) ],`

# --- 
# install pyenv -- not required, but is what I use locally. To be tested with --user/global installation or venv
pyenv install 3.11.7
pyenv virtualenv 3.11.7 anarci
pyenv activate anarci
# ---

pip install openmm biopython

python setup.py install