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License: MIT License
Hello,
Is possible to use as input CRAM rather than BAM files?
Thanks,
Mike
FFPolish appears to be written for version 3.8 (the new := operator was used), but requires version 3.7.8
When I tried to install FFPolish with python version 3.8, I get an error:
Looking for: ['ffpolish', 'python=3.8']
Encountered problems while solving:
When I installed FFPolish with python version 3.7.8, I get an error when I attempt to use FFPolish
(base) bash-4.4$ conda activate ffpolish
(ffpolish) bash-4.4$ which ffpolish
/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/bin/ffpolish
(ffpolish) bash-4.4$ python --version
Python 3.7.8
(ffpolish) bash-4.4$ ffpolish --help
Traceback (most recent call last):
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/bin/ffpolish", line 5, in
from filter import filter
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/bin/filter.py", line 11, in
import vaex
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/vaex/init.py", line 40, in
import vaex.dataframe
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/vaex/dataframe.py", line 17, in
import vaex.utils
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/vaex/utils.py", line 19, in
import progressbar
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/progressbar/init.py", line 5, in
from .bar import DataTransferBar
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/progressbar/bar.py", line 13, in
from python_utils import types
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/python_utils/init.py", line 1, in
from . import (
File "/scratch/users/astar/gis/simngl/apps/bcbio/v129/anaconda/envs/ffpolish/lib/python3.7/site-packages/python_utils/converters.py", line 89
if match := regexp.search(input_):
^
SyntaxError: invalid syntax
I am trying to install FFPolish using conda v22.9 (conda install -c matnguyen ffpolish) but it keeps loading for a long time without success (see output below). I have tried installing on it different machines without success. I believe my conda installation is fine as I use it without issues otherwise.
$ conda install -c matnguyen ffpolish
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
I have the necessary channels configured:
$ conda config --show channels
channels:
- conda-forge
- bioconda
- defaults
Is it possible to directly download the FFPolish repository from Github and install using this script: https://github.com/morinlab/FFPolish/blob/master/conda/build.sh?
cli.py filter
requires vcf2bed, which is provided by the bedops
package, but is not installed by default through conda
Hi what is the license on this code and can you please include it in the repo?
Hi, thank you very much for providing this tool. It might be quite useful.
Can you please let me know if it also handles INDELs in the input FFPE VCF or only works with SNVs?
Thanks!
Won-Chul
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