Installation issue
ObliviousMonkey opened this issue · 2 comments
I'm having trouble installing svviz2
on an Ubuntu 19.04 VM.
I've created a "mantaEnv" virtual environment using virtualenv
, used the recommended pip
command to install, tested it with svviz2 --help
and that's where things go wrong. Force reinstalling genomeview
doesn't change the error which keeps coming back.
What am I doing wrong ?
EDIT: I've installed Cython
in the virtualenv as per this thread, then force reinstalled both genomeview
and svviz2
, but the same error keeps popping up when doing svviz2 --help
. I'm listing pip list
output for reference after the chunk below.
(mantaEnv) discodingo@dVM:~$ pip install -U git+git://github.com/nspies/svviz2.git
Collecting git+git://github.com/nspies/svviz2.git
Cloning git://github.com/nspies/svviz2.git to /tmp/pip-req-build-hadhongy
Running command git clone -q git://github.com/nspies/svviz2.git /tmp/pip-req-build-hadhongy
Requirement already satisfied, skipping upgrade: pysam>=0.10 in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (0.15.3)
Requirement already satisfied, skipping upgrade: numpy>=1.11.1 in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (1.17.1)
Requirement already satisfied, skipping upgrade: pyfaidx in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (0.5.5.2)
Requirement already satisfied, skipping upgrade: tqdm in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (4.35.0)
Requirement already satisfied, skipping upgrade: pandas in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (0.25.1)
Requirement already satisfied, skipping upgrade: seqlib>=0.0.6 in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (0.0.6)
Requirement already satisfied, skipping upgrade: genomeview in ./mantaEnv/lib/python3.7/site-packages (from svviz2==2.0a3) (1.0.1)
Requirement already satisfied, skipping upgrade: setuptools>=0.7 in ./mantaEnv/lib/python3.7/site-packages (from pyfaidx->svviz2==2.0a3) (41.2.0)
Requirement already satisfied, skipping upgrade: six in ./mantaEnv/lib/python3.7/site-packages (from pyfaidx->svviz2==2.0a3) (1.12.0)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.6.1 in ./mantaEnv/lib/python3.7/site-packages (from pandas->svviz2==2.0a3) (2.8.0)
Requirement already satisfied, skipping upgrade: pytz>=2017.2 in ./mantaEnv/lib/python3.7/site-packages (from pandas->svviz2==2.0a3) (2019.2)
Requirement already satisfied, skipping upgrade: pybind11>=1.7 in ./mantaEnv/lib/python3.7/site-packages (from seqlib>=0.0.6->svviz2==2.0a3) (2.3.0)
Building wheels for collected packages: svviz2
Building wheel for svviz2 (setup.py) ... done
Created wheel for svviz2: filename=svviz2-2.0a3-cp37-cp37m-linux_x86_64.whl size=202123 sha256=ae52f1c301372450318126eda61acc099244be7defc23d1ff5b5596db917d011
Stored in directory: /tmp/pip-ephem-wheel-cache-4u95mbt8/wheels/f1/04/34/efbc0aafd8423c3c574c4f15164ac914dc3d8027a8153fceec
Successfully built svviz2
Installing collected packages: svviz2
Successfully installed svviz2-2.0a3
(mantaEnv) discodingo@dVM:~$ svviz2 --help
ssw library not found
ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview:
pip install --upgrade --force-reinstall genomeview
Traceback (most recent call last):
File "/home/discodingo/mantaEnv/bin/svviz2", line 6, in <module>
from svviz2.app.main import main
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/svviz2/app/main.py", line 7, in <module>
from svviz2.visualize import visualize
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/svviz2/visualize/visualize.py", line 8, in <module>
from genomeview import Document, ViewRow, GenomeView
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/genomeview/__init__.py", line 24, in <module>
from genomeview.bamtrack import *
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/genomeview/bamtrack.py", line 6, in <module>
from genomeview import MismatchCounts
ImportError: cannot import name 'MismatchCounts' from 'genomeview' (/home/discodingo/mantaEnv/lib/python3.7/site-packages/genomeview/__init__.py)
(mantaEnv) discodingo@dVM:~$ pip install --upgrade --force-reinstall genomeview
Collecting genomeview
Collecting numpy (from genomeview)
Using cached https://files.pythonhosted.org/packages/25/eb/4ecf6b13897391cb07a4231e9d9c671b55dfbbf6f4a514a1a0c594f2d8d9/numpy-1.17.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting pysam (from genomeview)
Installing collected packages: numpy, pysam, genomeview
Found existing installation: numpy 1.17.1
Uninstalling numpy-1.17.1:
Successfully uninstalled numpy-1.17.1
Found existing installation: pysam 0.15.3
Uninstalling pysam-0.15.3:
Successfully uninstalled pysam-0.15.3
Found existing installation: genomeview 1.0.1
Uninstalling genomeview-1.0.1:
Successfully uninstalled genomeview-1.0.1
Successfully installed genomeview-1.0.1 numpy-1.17.1 pysam-0.15.3
(mantaEnv) discodingo@dVM:~$ svviz2 --help
ssw library not found
ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview:
pip install --upgrade --force-reinstall genomeview
Traceback (most recent call last):
File "/home/discodingo/mantaEnv/bin/svviz2", line 6, in <module>
from svviz2.app.main import main
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/svviz2/app/main.py", line 7, in <module>
from svviz2.visualize import visualize
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/svviz2/visualize/visualize.py", line 8, in <module>
from genomeview import Document, ViewRow, GenomeView
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/genomeview/__init__.py", line 24, in <module>
from genomeview.bamtrack import *
File "/home/discodingo/mantaEnv/lib/python3.7/site-packages/genomeview/bamtrack.py", line 6, in <module>
from genomeview import MismatchCounts
ImportError: cannot import name 'MismatchCounts' from 'genomeview' (/home/discodingo/mantaEnv/lib/python3.7/site-packages/genomeview/__init__.py)
(mantaEnv) discodingo@vm:~$ pip list
Package Version
------------------ -------
atomicwrites 1.3.0
attrs 19.1.0
cffi 1.12.3
Cython 0.29.13
genomeview 1.0.1
genosv 0.3.0
importlib-metadata 0.20
Jinja2 2.10.1
MarkupSafe 1.1.1
more-itertools 7.2.0
numpy 1.17.1
packaging 19.1
pandas 0.25.1
pip 19.2.3
pluggy 0.12.0
py 1.8.0
pybind11 2.3.0
pycparser 2.19
pyfaidx 0.5.5.2
pyparsing 2.4.2
pysam 0.15.3
pytest 5.1.2
python-dateutil 2.8.0
pytz 2019.2
rpy2 3.1.0
seqlib 0.0.6
setuptools 41.2.0
simplegeneric 0.8.1
six 1.12.0
svviz2 2.0a3
tqdm 4.35.0
tzlocal 2.0.0
wcwidth 0.1.7
wheel 0.33.6
zipp 0.6.0
@ObliviousMonkey I was experiencing the same issue on RHEL 6/7.
In my case the underlying issue was genomeview having issues cythonizing files, which resulted in a segfault. I got around that by downloading the genomeview source and manually installing it into the environment.
virtualenv svviz2-2.0a
source svviz2-2.0a
mkdir svviz2-2.0a/src
cd svviz2-2.0a/src
wget https://github.com/nspies/genomeview/archive/v1.0.1.tar.gz
tar -zxf v1.0.1.tar.gz
cd genomeview-1.0.1
python setup.py install
I didn't get any errors at this point in my miniconda3 environment but I did get this error inside a virtualenv:
cythoning genomeview/_quickconsensus.pyx to genomeview/_quickconsensus.c
Segmentation fault (core dumped)
After running python setup.py install
again it seems to install just fine.
python setup.py install
pip install -U git+git://github.com/nspies/svviz2.git
svviz2
It seems that cythonizing that file only fails the first time around and not the second. I think the build gets cleaned up by pip after it fails, but not with the setuptools installation method. Maybe there are dependencies that are not found the first time around?
@cenders This approach did not initially work for me in virtualenv
.
I then made a miniconda3
env, where the same approach did not work either. However force reinstalling genomeview
through pip
finally solved it for me, I don't know why:
pip install -U --force-reinstall git+https://github.com/nspies/genomeview.git
Thank you!!