Installation issues / suggestions / solutions

[hegelab]

Sorry, not a full instruction, but should work something like that:

conda create -p /sopt/epyc/miniconda/envs/anarci_env python=3.10 -y
conda activate anarci_env
conda install -c conda-forge biopython -y
conda install -c bioconda hmmer=3.3.2 -y
conda install -c bioconda muscle=3.8.1551 -y

manual steps

git clone
cd ANARCI/build_pipeline
mv curated_alignments/germlines.py ../lib/python/anarci/
./RUN_pipeline.sh
mkdir your_conda/envs/anarci_env/lib/python3.10/site-packages/anarci/dat/
cp -r HMMs your_conda/envs/anarci_env/lib/python3.10/site-packages/anarci/dat/
cd ..

edit setup.py commenting out most of the CustomInstallCommand

   # Build HMMs from IMGT germlines
   # os.chdir("build_pipeline")
   # print('INFO: Downloading germlines from IMGT and building HMMs...')
   # print("INFO: running 'RUN_pipeline.sh', this will take a couple a minutes.")
   # proc = subprocess.Popen(["bash", "RUN_pipeline.sh"], stdout = subprocess.PIPE, stderr = subprocess.PIPE)
   # o, e = proc.communicate()

   # print(o.decode())
   # print(e.decode())
   
   # Copy HMMs where ANARCI can find them
   # shutil.copy( "curated_alignments/germlines.py", ANARCI_LOC )
   # os.mkdir(os.path.join(ANARCI_LOC, "dat"))
   # shutil.copytree( "HMMs", os.path.join(ANARCI_LOC, "dat/HMMs/") )
  
   # Remove data from HMMs generation
   # try:
   #     shutil.rmtree("curated_alignments/")
   #     shutil.rmtree("muscle_alignments/")
   #     shutil.rmtree("HMMs/")
   #     shutil.rmtree("IMGT_sequence_files/")
   # except OSError:
   #     pass

finally run:
pip install .