Escape prediction experiments

[ghost]

Hi,

First, I would like to thank you for inventing such an awesome program.

I would like to ask a question about running the escape prediction experiments using a FASTA file. I installed all the required dependencies and replicated the escape prediction experiments following the description in cov_fasta.md file. However, the got the errors as followed:

"
Traceback (most recent call last):
File "bin/cov_fasta.py", line 1, in
from mutation import *
File "/scratch/panbazha/ngoquoc1/viral-mutation/bin/mutation.py", line 1, in
from utils import *
File "/scratch/panbazha/ngoquoc1/viral-mutation/bin/utils.py", line 12, in
import scanpy as sc
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/scanpy/init.py", line 39, in
from . import datasets, logging, queries, external, get
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/scanpy/external/init.py", line 3, in
from . import pp
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/scanpy/external/pp/init.py", line 4, in
from ._magic import magic
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/scanpy/external/pp/_magic.py", line 8, in
from legacy_api_wrap import legacy_api
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/legacy_api_wrap.py", line 18, in
from get_version import get_version
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/get_version/init.py", line 287, in
version = get_version(file, vcs="git")
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/get_version/init.py", line 270, in get_version
version = method(parent)
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/get_version/init.py", line 117, in get_version_from_vcs
vcs_root = find_vcs_root(parent, vcs=vcs)
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/site-packages/get_version/init.py", line 162, in find_vcs_root
ret = run(cmd, cwd=start, capture_output=True)
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/subprocess.py", line 488, in run
with Popen(*popenargs, **kwargs) as process:
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/subprocess.py", line 800, in init
restore_signals, start_new_session)
File "/scratch/panbazha/ngoquoc1/anaconda3/envs/viral-mutation/lib/python3.7/subprocess.py", line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'git': 'git'
"
Do you have any idea what is the source of problem? Thank you so much for your attention.

Best regards,

[brianhie]

Looks like a problem with the environment -- can you make sure git is installed? E.g., I googled the error message and found this: anapaulagomes/pytest-picked#16

[ghost]

Hi,

Yes, you were correct. I did not install git when creating environment. Thank you a lot for your support.

Best regards,