Singularity Image is broken

[just-simon-5]

Hi @wheaton5,

The singularity image in the latest release that you host on google drive is broken. The path looks like:

/miniconda3/bin:/miniconda3/condabin:/miniconda3/bin:/opt/minimap2-2.26_x64-linux:/opt/bedtools-2:/opt/freebayes/build:/opt/hisat2-2.2.1:/opt/bedtools2/bin:/opt/souporcell:/opt/souporcell/troublet/target/release:/usr/local/condabin:/opt/minimap2-2.26_x64-linux:/root/.cargo/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 

however looking inside the image, bedtools is actually located here:

/bedtools2/bin/

Thanks,
Simon

[wheaton5]

huh, i thought i tested it and it worked, but this does appear to be correct. rebuilding image now.

[wheaton5]

There are always issues with updating the singularity build. Ran into two so far... I'll update here when done and tested.

[Thapeachydude]

I've tried running the 2.5 image, but had this error (2.0 works fine).

 File "/opt/souporcell/souporcell_pipeline.py", line 584, in <module>
    final_vcf = freebayes(args, bam, fasta)
  File "/opt/souporcell/souporcell_pipeline.py", line 385, in freebayes
    subprocess.check_call(["bedtools", "merge", "-i", depth_file], stdout = bed)
  File "/miniconda3/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/miniconda3/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/miniconda3/lib/python3.10/subprocess.py", line 971, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/miniconda3/lib/python3.10/subprocess.py", line 1863, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: 'bedtools'

[plijnzaad]

I'm having the same problem:

Traceback (most recent call last):
File "/opt/souporcell/souporcell_pipeline.py", line 584, in
final_vcf = freebayes(args, bam, fasta)
File "/opt/souporcell/souporcell_pipeline.py", line 385, in freebayes
subprocess.check_call(["bedtools", "merge", "-i", depth_file], stdout = bed)
File "/miniconda3/lib/python3.10/subprocess.py", line 364, in check_call
retcode = call(*popenargs, **kwargs)
File "/miniconda3/lib/python3.10/subprocess.py", line 345, in call
with Popen(*popenargs, **kwargs) as p:
File "/miniconda3/lib/python3.10/subprocess.py", line 971, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/miniconda3/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: 'bedtools'

This is also using the V2.5 singularity image. The V2.0 doesn't have that problem (but there I run into issue #175 ).