metasv
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Pip installation error
I'm trying to set up metaSV
on a shared HPC on ComputeCanada's Cedar and running into an error with the pip
installation.
Following the installation instructions I download/load the system requirements first.
First load provided modules
and setup Python env
:
module load python/3.8
module load spades/3.13.1
module load samtools/0.1.20
virtualenv metaSV
source metaSV/bin/activate
pip install Cython # needs to be installed before the following 3 dependencies
pip install pysam
pip install pybedtools
pip install pyvcf
SPAdes
was already available but I needed to downloaded/compiled AGE make OMP=no
Now I try to install metaSV
with pip install https://github.com/bioinform/metasv/archive/0.5.2.tar.gz
and get an error:
Ignoring pip: markers 'python_version < "3"' don't match your environment
Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic
Collecting https://github.com/bioinform/metasv/archive/0.5.2.tar.gz
Using cached https://github.com/bioinform/metasv/archive/0.5.2.tar.gz
ERROR: Command errored out with exit status 1:
command: /project/6013424/common/tools/CNV/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-pd08her8/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-pd08her8/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-req-build-pd08her8/pip-egg-info
cwd: /tmp/pip-req-build-pd08her8/
Complete output (6 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-req-build-pd08her8/setup.py", line 8
print version
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(version)?
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
My uname -a
:
Linux cedar1.cedar.computecanada.ca 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 GNU/Linux