an error when running on Docker

Hi, Thanks for your work! I moved reads/annotations directory to analysis directory and edit files meta.csv and var.py as mentioned in README and I ran below command docker run -u `id -u` --rm -it -v $(pwd):/data egaffo/circompara2:v0.1.2.1 However, I got below error:

TypeError: Tried to lookup Dir 'dbs/indexes' as a File.:
  File "/circompara2/src/sconstructs/main.py", line 489:
    exports = '''env_check_indexes''')
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 660:
    return method(*args, **kw)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 597:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 286:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/circompara2/src/sconstructs/check_indexes.py", line 118:
    exports = '''env_build_indexes ''')
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 660:
    return method(*args, **kw)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 597:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 286:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/circompara2/src/sconstructs/build_indexes.py", line 60:
    env_index_hisat2['GENOME'] = ','.join([File(f).abspath for f in env['GENOME'].split(',')])
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 660:
    return method(*args, **kw)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Environment.py", line 2092:
    return self.fs.File(s, *args, **kw)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 1382:
    return self._lookup(name, directory, File, create)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 1361:
    return root._lookup_abs(p, fsclass, create)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 2406:
    result.must_be_same(klass)
  File "/circompara2/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 618:
    (self.__class__.__name__, self.get_internal_path(), klass.__name__))```

```var.py
META            = 'meta.csv'
GENOME_FASTA    = '/annotation/CFLAR_HIPK3.fa'
ANNOTATION      = '/annotation/CFLAR_HIPK3.gtf' 
CPUS            = '4'

file,sample,adapter  
/reads/readsA_1.fastq.gz,sample_A,/circompara2/tools/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa  
/reads/readsA_2.fastq.gz,sample_A,/circompara2/tools/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa  
/reads/readsB_1.fastq.gz,sample_B,/circompara2/tools/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa  
/reads/readsB_2.fastq.gz,sample_B,/circompara2/tools/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa

It only generated an empty directory dbs, and my system is macOS .what did I miss? Appreciated with any reply. Thank u.

egaffo / circompara2

an error when running on Docker #2