Dear All,
I have got this error when I try to install Cryosparc, any suggestions how to solve it?
The cryoSPARC System master installation will host a database,
web application, and command layer for cryoSPARC, but will not
perform processing jobs.
Please read and confirm the above settings. The cryoSPARC database
will be stored at the database directory which is relative to the
root directory, unless provided as an absolute path.
You can change the database directory now by passing the --dbapth
parameter to this installer, or later via the command line.
Are the above settings correct?
1) Yes
2) No
#? 1
Continuing.
******************************************************************
Setting up hard-coded config.sh environment variables
******************************************************************
Installing all dependencies.
Checking dependencies...
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
Installing anaconda python...
------------------------------------------------------------------------
PREFIX=${HOME}/cryosparc2_master/deps/anaconda
installing: python-2.7.16-h9bab390_0 ...
Python 2.7.16 :: Anaconda, Inc.
installing: ca-certificates-2019.1.23-0 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1b-h7b6447c_1 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: libedit-3.1.20181209-hc058e9b_0 ...
installing: readline-7.0-h7b6447c_5 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: sqlite-3.27.2-h7b6447c_0 ...
installing: asn1crypto-0.24.0-py27_0 ...
installing: certifi-2019.3.9-py27_0 ...
installing: chardet-3.0.4-py27_1 ...
installing: enum34-1.1.6-py27_1 ...
installing: futures-3.2.0-py27_0 ...
installing: idna-2.8-py27_0 ...
installing: ipaddress-1.0.22-py27_0 ...
installing: pycosat-0.6.3-py27h14c3975_0 ...
installing: pycparser-2.19-py27_0 ...
installing: pysocks-1.6.8-py27_0 ...
installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...
installing: six-1.12.0-py27_0 ...
installing: cffi-1.12.2-py27h2e261b9_1 ...
installing: setuptools-41.0.0-py27_0 ...
installing: cryptography-2.6.1-py27h1ba5d50_0 ...
installing: wheel-0.33.1-py27_0 ...
installing: pip-19.0.3-py27_0 ...
installing: pyopenssl-19.0.0-py27_0 ...
installing: urllib3-1.24.1-py27_0 ...
installing: requests-2.21.0-py27_0 ...
installing: conda-4.6.14-py27_0 ...
installation finished.
------------------------------------------------------------------------
Done.
anaconda python installation successful.
------------------------------------------------------------------------
Preparing to install all conda packages...
------------------------------------------------------------------------
${HOME}/cryosparc2_master/deps/anaconda/bin/conda: line 6: syntax error near unexpected token `sys.argv'
${HOME}/cryosparc2_master/deps/anaconda/bin/conda: line 6: `if len(sys.argv) > 1 and sys.argv[1].startswith('shell.') and sys.path and sys.path[0] == '':'
------------------------------------------------------------------------
Done.
conda packages installation successful.
------------------------------------------------------------------------
Preparing to install all pip packages...
------------------------------------------------------------------------
from: can't read /var/mail/pip._internal
${HOME}/cryosparc2_master/deps/anaconda/bin/pip: line 10: syntax error near unexpected token `('
${HOME}/cryosparc2_master/deps/anaconda/bin/pip: line 10: ` sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])'
------------------------------------------------------------------------
Done.
pip packages installation successful.
------------------------------------------------------------------------
Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling...
------------------------------------------------------------------------
mongodb 3.4.10 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
CryoSPARC System master has now been installed.
Add bin directory to your ~/.bashrc ?
1) Yes
2) No
#? 2
To run cryosparc, be sure to add "${HOME}/cryosparc2_master/bin" to your path
or add a symlink to "${HOME}/cryosparc2_master/bin/cryosparcm" to your path.
Please re-start your terminal shell to make the cryosparcm
command available.
Afterwards, you can start this master instance with:
$ cryosparcm start
To find out about other available commands, use:
$ cryosparcm help
In order to run processing jobs, you will also need to install
one or more cryoSPARC worker nodes and connect them to this
master node.
${HOME}/cryosparc2_master/bin/cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named pymongo