install sniffles2 issues

[guandailu]

I try to install sniffles2 using different strategies, but all failed:

1. 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 ImportError in system pip wrappers after an upgrade pypa/pip#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

2. 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'

3. 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.

[fritzsedlazeck]

Do you have python 3 installed ?
Thx
Fritz

[guandailu]

I test the version:
python --version
Python 3.8.13

[fritzsedlazeck]

ok my last guess: pysam ?
Other than that we would need to look into what would cause this..
Thanks
Fritz

[guandailu]

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\ :

[danrdanny]

I had a similar error. conda install python=3.7 followed by conda install sniffles=2.0 worked for me.

[guandailu]

Thank you so much! It also works me!