Incorporate HUNePi

[GopiGugan]

• 472

[GopiGugan]

• Need to update INSTALL.md with R Dependencies
  • tidyquant
  • yaml
  • matrixStats
  • ape
  • optparse
  • phytools
  • devtools
  • LambdaSkyline
• Add rpy2 and pyyaml to list of dependencies

[GopiGugan]

Traceback (most recent call last):
  File "/home/covizu/covizu/batch.py", line 160, in <module>
    result, infection_prediction = make_beadplots(by_lineage, args, cb.callback, t0=cb.t0.timestamp())
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/covizu/covizu/covizu/utils/batch_utils.py", line 399, in make_beadplots
    cne = find_Ne(ctree, 'clabels_file.csv', False)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/covizu/covizu/covizu/utils/batch_utils.py", line 211, in find_Ne
    Ne = subprocess.Popen("Rscript " + os.path.dirname(__file__) + "/skyline_est.R -t " + 
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.11/subprocess.py", line 1024, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib64/python3.11/subprocess.py", line 1816, in _execute_child
    errpipe_read, errpipe_write = os.pipe()
                                  ^^^^^^^^^
OSError: [Errno 24] Too many open files

We were not closing the temporary files that were being created. Fixed after closing them

[GopiGugan]

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