Sniffles
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install sniffles2 issues
I try to install sniffles2 using different strategies, but all failed:
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pip install sniffles, see error: WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. To avoid this problem you can invoke Python with '-m pip' instead of running pip directly. Defaulting to user installation because normal site-packages is not writeable ERROR: Could not find a version that satisfies the requirement sniffles (from versions: none) ERROR: No matching distribution found for sniffles
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conda install -c bioconda sniffles=2.0 -n sniffles -m, then run sniffles -h, see error: Traceback (most recent call last): File "/home/dguan/anaconda3/envs/sniffles/bin/sniffles", line 33, in
from sniffles import parallel File "/home/dguan/anaconda3/envs/sniffles/lib/python3.8/site-packages/sniffles/parallel.py", line 17, in from sniffles import leadprov File "/home/dguan/anaconda3/envs/sniffles/lib/python3.8/site-packages/sniffles/leadprov.py", line 137, in OPTAB={pysam.CMATCH: (1,1,0), AttributeError: module 'pysam' has no attribute 'CMATCH' -
install sniffles 1 first in conda, then update to 2 conda install -c bioconda sniffles -n sniffles -m, then conda update -c bioconda sniffles, then run sniffles -h
Usage: sniffles [options] -m <sorted.bam> -v <output.vcf> Version: 1.0.12 Contact: [email protected]
Not update it.
Do you have python 3 installed ? Thx Fritz
I test the version: python --version Python 3.8.13
ok my last guess: pysam ? Other than that we would need to look into what would cause this.. Thanks Fritz
The installed pysam is:
pysam bioconda/linux-64::pysam-0.9.1-py38hd1a2d5f_10
Then I try to install a higher version: conda install -c bioconda pysam=0.16.0.1 Unfortunately, there are a lot of conflicts: Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining conflict for wheel libssh2 pysam setuptools sniffles python_abi samtools openssl krb5 curl htslib libcurl pip python bcftoo\ :
I had a similar error. conda install python=3.7
followed by conda install sniffles=2.0
worked for me.
Thank you so much! It also works me!