Cryosparc: command not found

Hi all,

apologies for being a linux noob. I’ve been trying to install cryosparc and keep running into the same 2 errors:

“Cannot uninstall ‘PyYAML’. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.”

and cryosparc start returns “cryosparc: command not found”. please help!

thanks!

Here’s the full installation output:

======================================================
cryoSPARC Download Script

CryoSPARC by default will install to your home directory
at the following path:
/home/dgl/cryosparc
Ideally, this path should be on reliable redundant storage
because this is where cryoSPARC will store its internal
database. Result data files (maps, micrographs, etc) will
be stored at a different location that you can select
later during configuration. You will also be asked for a
path to an SSD cache directory during configuration.

Continue installation at
/home/dgl/cryosparc

  1. Yes
  2. Change
    #? 1

Installing at
/home/dgl/cryosparc

Downloading latest cryoSPARC distribution…
Done.

Extracting…
Done.

Starting cryoSPARC installer…
Found curl at /usr/bin/curl
******* CRYOSPARC INSTALLER **************************************

Installation Settings:
Root Directory : /home/dgl/cryosparc
HTTP Port Number : 38000
MongoDB Port Number: 38001
Install Type : master
Developer Install : false
Operating System : Linux
Insecure Install : false
Deploy Version : v0.6.5


Please read and confirm the above settings. Note that the cryosparc
root directory is the location where cryosparc will store its internal
database and settings, but not input data or results.
The root directory should ideally not be on your SSDs. You will be
asked later on during configuration to specify a path to an SSD that
will be used as a cache for input data.

Are the above settings correct?

  1. Yes
  2. No
    #? 1
    Continuing.
    ==================================================================
    Checking for CUDA
    ==================================================================
    Found nvidia-smi at /usr/bin/nvidia-smi
    Found nvcc at /usr/bin/nvcc
    CUDA check successful.
    ==================================================================
    Installing Node 4.6.2
    ==================================================================
    Checking for previous version of node js…
    Installing Node locally
    Downloading and installing…


Complete.
NodeJS installation successful.

Installing MongoDB

Checking for previous version of mongo…
Downloading…
Done.
Installing…
Done.
MongoDB installation successful.

Checking for Python (Anaconda)

Unable to find conda.
Installing local python.

Installing Python (Anaconda)

Downloading…
Done.
Installing…

PREFIX=/home/dgl/cryosparc/anaconda2
installing: python-2.7.15-h1571d57_0 …
Python 2.7.15 :: Anaconda, Inc.
installing: ca-certificates-2018.03.07-0 …
installing: conda-env-2.6.0-h36134e3_1 …
installing: libgcc-ng-7.2.0-hdf63c60_3 …
installing: libstdcxx-ng-7.2.0-hdf63c60_3 …
installing: libffi-3.2.1-hd88cf55_4 …
installing: ncurses-6.1-hf484d3e_0 …
installing: openssl-1.0.2o-h20670df_0 …
installing: tk-8.6.7-hc745277_3 …
installing: yaml-0.1.7-had09818_2 …
installing: zlib-1.2.11-ha838bed_2 …
installing: libedit-3.1.20170329-h6b74fdf_2 …
installing: readline-7.0-ha6073c6_4 …
installing: sqlite-3.23.1-he433501_0 …
installing: asn1crypto-0.24.0-py27_0 …
installing: certifi-2018.4.16-py27_0 …
installing: chardet-3.0.4-py27hfa10054_1 …
installing: enum34-1.1.6-py27h99a27e9_1 …
installing: futures-3.2.0-py27h7b459c0_0 …
installing: idna-2.6-py27h5722d68_1 …
installing: ipaddress-1.0.22-py27_0 …
installing: pycosat-0.6.3-py27ha4109ae_0 …
installing: pycparser-2.18-py27hefa08c5_1 …
installing: pysocks-1.6.8-py27_0 …
installing: ruamel_yaml-0.15.37-py27h14c3975_2 …
installing: six-1.11.0-py27h5f960f1_1 …
installing: cffi-1.11.5-py27h9745a5d_0 …
installing: setuptools-39.2.0-py27_0 …
installing: cryptography-2.2.2-py27h14c3975_0 …
installing: wheel-0.31.1-py27_0 …
installing: pip-10.0.1-py27_0 …
installing: pyopenssl-18.0.0-py27_0 …
installing: urllib3-1.22-py27ha55213b_0 …
installing: requests-2.18.4-py27hc5b0589_1 …
installing: conda-4.5.4-py27_0 …
installation finished.

Done.
Python installation successful.

Install/Update Python Packages


Solving environment: …working… done

Package Plan

environment location: /home/dgl/cryosparc/anaconda2

added / updated specs:
- conda

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
openssl-1.0.2o             |       h14c3975_1         3.4 MB
conda-4.5.9                |           py27_0         1.0 MB
------------------------------------------------------------
                                       Total:         4.5 MB

The following packages will be UPDATED:

conda:   4.5.4-py27_0      --> 4.5.9-py27_0     
openssl: 1.0.2o-h20670df_0 --> 1.0.2o-h14c3975_1

Preparing transaction: …working… done
Verifying transaction: …working… done
Executing transaction: …working… done
Solving environment: …working… done

All requested packages already installed.

Solving environment: …working… done

Package Plan

environment location: /home/dgl/cryosparc/anaconda2

added / updated specs:
- cython=0.25.1
- future=0.15.2
- ipython=5.1.0
- jinja2=2.8
- matplotlib=1.5.1
- numba=0.36.2
- numexpr=2.6.1
- numpy=1.11.2
- pandas=0.21.0
- scikit-image=0.13.1
- scipy=0.18.1

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
traitlets-4.3.2            |           py27_0         128 KB
pexpect-4.6.0              |           py27_0          74 KB
bokeh-0.13.0               |           py27_0         5.1 MB
pillow-4.2.1               |           py27_0         843 KB
partd-0.3.8                |           py27_0          30 KB
packaging-17.1             |           py27_0          32 KB
xz-5.2.4                   |       h14c3975_4         366 KB
toolz-0.9.0                |           py27_0          90 KB
matplotlib-1.5.1           |      np111py27_0         8.4 MB
libtiff-4.0.9              |       he85c1e1_1         566 KB
ipython-5.1.0              |           py27_0         936 KB
qt-4.8.7                   |                3        34.1 MB
pathlib2-2.3.2             |           py27_0          31 KB
olefile-0.45.1             |           py27_0          47 KB
scikit-image-0.13.1        |   py27h14c3975_1        23.2 MB
numba-0.36.2               |np111py27haafad4c_0         2.2 MB
locket-0.2.0               |           py27_1           8 KB
distributed-1.22.1         |           py27_0         768 KB
mkl-11.3.3                 |                0       122.1 MB
future-0.15.2              |           py27_0         616 KB
cytoolz-0.9.0.1            |   py27h14c3975_1         410 KB
freetype-2.5.5             |                2         2.5 MB
get_terminal_size-1.0.0    |       haa9412d_0           3 KB
python-dateutil-2.7.3      |           py27_0         258 KB
heapdict-1.0.0             |           py27_2           8 KB
sortedcontainers-2.0.4     |           py27_0          41 KB
tblib-1.3.2                |           py27_0          16 KB
wcwidth-0.1.7              |           py27_0          25 KB
pyyaml-3.13                |   py27h14c3975_0         173 KB
backports.shutil_get_terminal_size-1.0.0|           py27_2           8 KB
libgfortran-3.0.0          |                1         281 KB
click-6.7                  |           py27_0         103 KB
msgpack-python-0.5.6       |   py27h6bb024c_1          99 KB
ipython_genutils-0.2.0     |           py27_0          38 KB
pygments-2.2.0             |   py27h4a8b6f5_0         1.3 MB
libiconv-1.14              |                0         2.0 MB
pyparsing-2.2.0            |           py27_1          94 KB
tornado-5.0.2              |   py27h14c3975_0         627 KB
ptyprocess-0.6.0           |           py27_0          22 KB
pandas-0.21.0              |   py27he307072_1        10.5 MB
cairo-1.14.8               |                0         609 KB
backports_abc-0.5          |           py27_0          12 KB
decorator-4.3.0            |           py27_0          15 KB
icu-58.2                   |       h9c2bf20_1        22.5 MB
zict-0.1.3                 |           py27_0          17 KB
sip-4.18                   |           py27_0         264 KB
cycler-0.10.0              |           py27_0          13 KB
backports-1.0              |           py27_1           3 KB
numpy-1.11.2               |           py27_0         6.2 MB
funcsigs-1.0.2             |           py27_0          20 KB
dask-0.18.2                |           py27_0           3 KB
cython-0.25.1              |           py27_0         5.6 MB
jpeg-9b                    |       h024ee3a_2         248 KB
simplegeneric-0.8.1        |           py27_2           9 KB
psutil-5.4.6               |   py27h14c3975_0         297 KB
cloudpickle-0.5.3          |           py27_0          25 KB
jinja2-2.8.1               |           py27_0         278 KB
llvmlite-0.21.0            |   py27h6dad3f9_0        14.7 MB
pixman-0.34.0              |       hceecf20_3         598 KB
fontconfig-2.12.1          |                3         429 KB
networkx-2.1               |           py27_0         1.8 MB
libpng-1.6.34              |       hb9fc6fc_0         334 KB
dask-core-0.18.2           |           py27_0         1.1 MB
pycairo-1.13.3             |   py27hea6d626_0          54 KB
singledispatch-3.4.0.3     |           py27_0          15 KB
pickleshare-0.7.4          |           py27_0          11 KB
pytz-2018.5                |           py27_0         231 KB
prompt_toolkit-1.0.15      |           py27_0         333 KB
libxml2-2.9.8              |       h26e45fe_1         2.0 MB
numexpr-2.6.1              |      np111py27_1         347 KB
markupsafe-1.0             |   py27h14c3975_1          24 KB
scandir-1.8                |   py27h14c3975_0          27 KB
pywavelets-0.5.2           |   py27hecda097_0         4.0 MB
imageio-2.3.0              |           py27_0         3.3 MB
scipy-0.18.1               |      np111py27_0        30.9 MB
pyqt-4.11.4                |           py27_4         3.3 MB
------------------------------------------------------------
                                       Total:       317.5 MB

The following NEW packages will be INSTALLED:

backports:                          1.0-py27_1                
backports.shutil_get_terminal_size: 1.0.0-py27_2              
backports_abc:                      0.5-py27_0                
bokeh:                              0.13.0-py27_0             
cairo:                              1.14.8-0                  
click:                              6.7-py27_0                
cloudpickle:                        0.5.3-py27_0              
cycler:                             0.10.0-py27_0             
cython:                             0.25.1-py27_0             
cytoolz:                            0.9.0.1-py27h14c3975_1    
dask:                               0.18.2-py27_0             
dask-core:                          0.18.2-py27_0             
decorator:                          4.3.0-py27_0              
distributed:                        1.22.1-py27_0             
fontconfig:                         2.12.1-3                  
freetype:                           2.5.5-2                   
funcsigs:                           1.0.2-py27_0              
future:                             0.15.2-py27_0             
get_terminal_size:                  1.0.0-haa9412d_0          
heapdict:                           1.0.0-py27_2              
icu:                                58.2-h9c2bf20_1           
imageio:                            2.3.0-py27_0              
ipython:                            5.1.0-py27_0              
ipython_genutils:                   0.2.0-py27_0              
jinja2:                             2.8.1-py27_0              
jpeg:                               9b-h024ee3a_2             
libgfortran:                        3.0.0-1                   
libiconv:                           1.14-0                    
libpng:                             1.6.34-hb9fc6fc_0         
libtiff:                            4.0.9-he85c1e1_1          
libxml2:                            2.9.8-h26e45fe_1          
llvmlite:                           0.21.0-py27h6dad3f9_0     
locket:                             0.2.0-py27_1              
markupsafe:                         1.0-py27h14c3975_1        
matplotlib:                         1.5.1-np111py27_0         
mkl:                                11.3.3-0                  
msgpack-python:                     0.5.6-py27h6bb024c_1      
networkx:                           2.1-py27_0                
numba:                              0.36.2-np111py27haafad4c_0
numexpr:                            2.6.1-np111py27_1         
numpy:                              1.11.2-py27_0             
olefile:                            0.45.1-py27_0             
packaging:                          17.1-py27_0               
pandas:                             0.21.0-py27he307072_1     
partd:                              0.3.8-py27_0              
pathlib2:                           2.3.2-py27_0              
pexpect:                            4.6.0-py27_0              
pickleshare:                        0.7.4-py27_0              
pillow:                             4.2.1-py27_0              
pixman:                             0.34.0-hceecf20_3         
prompt_toolkit:                     1.0.15-py27_0             
psutil:                             5.4.6-py27h14c3975_0      
ptyprocess:                         0.6.0-py27_0              
pycairo:                            1.13.3-py27hea6d626_0     
pygments:                           2.2.0-py27h4a8b6f5_0      
pyparsing:                          2.2.0-py27_1              
pyqt:                               4.11.4-py27_4             
python-dateutil:                    2.7.3-py27_0              
pytz:                               2018.5-py27_0             
pywavelets:                         0.5.2-py27hecda097_0      
pyyaml:                             3.13-py27h14c3975_0       
qt:                                 4.8.7-3                   
scandir:                            1.8-py27h14c3975_0        
scikit-image:                       0.13.1-py27h14c3975_1     
scipy:                              0.18.1-np111py27_0        
simplegeneric:                      0.8.1-py27_2              
singledispatch:                     3.4.0.3-py27_0            
sip:                                4.18-py27_0               
sortedcontainers:                   2.0.4-py27_0              
tblib:                              1.3.2-py27_0              
toolz:                              0.9.0-py27_0              
tornado:                            5.0.2-py27h14c3975_0      
traitlets:                          4.3.2-py27_0              
wcwidth:                            0.1.7-py27_0              
xz:                                 5.2.4-h14c3975_4          
zict:                               0.1.3-py27_0              

Preparing transaction: …working… done
Verifying transaction: …working… done
Executing transaction: …working… done
Solving environment: …working… done

Package Plan

environment location: /home/dgl/cryosparc/anaconda2

added / updated specs:
- fftw=3.3.7
- pyfftw=0.10.4

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
certifi-2018.4.16          |           py27_0         142 KB  conda-forge
openssl-1.0.2o             |       h470a237_1         3.5 MB  conda-forge
ca-certificates-2018.4.16  |                0         139 KB  conda-forge
fftw-3.3.7                 |       h470a237_1         3.8 MB  conda-forge
pyfftw-0.10.4              |   py27h7eb728f_3         2.1 MB  conda-forge
conda-4.5.9                |           py27_0         634 KB  conda-forge
------------------------------------------------------------
                                       Total:        10.3 MB

The following NEW packages will be INSTALLED:

fftw:            3.3.7-h470a237_1      conda-forge
pyfftw:          0.10.4-py27h7eb728f_3 conda-forge

The following packages will be UPDATED:

ca-certificates: 2018.03.07-0                      --> 2018.4.16-0       conda-forge
certifi:         2018.4.16-py27_0                  --> 2018.4.16-py27_0  conda-forge
conda:           4.5.9-py27_0                      --> 4.5.9-py27_0      conda-forge
openssl:         1.0.2o-h14c3975_1                 --> 1.0.2o-h470a237_1 conda-forge

Preparing transaction: …working… done
Verifying transaction: …working… done
Executing transaction: …working… done
Collecting pylbfgs==0.2.0.3
Using cached (https)://files.pythonhosted.org/packages/82/3a/1f6eacc68ad1125efbdcd5dca004cf6ef3bbd3cafc28bb98e2d6b68a2bb0/PyLBFGS-0.2.0.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pyyaml==3.12
Collecting diskcache==2.0.2
Using cached (https)://files.pythonhosted.org/packages/e7/2a/68d9fcbe34cbbf042af49007d399411928bd489cc9f261954564764b7e72/diskcache-2.0.2-py2.py3-none-any.whl
Collecting pymongo==3.3.1
Using cached (https)://files.pythonhosted.org/packages/9c/61/717a898d6f370666dcc60f9bf3724d4215ce4fc80e8871bbb7f96d94ab41/pymongo-3.3.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting nvidia-ml-py==7.352.0
Collecting pycrypto==2.6.1
Collecting psutil==4.4.2
Requirement already satisfied: numpy in ./anaconda2/lib/python2.7/site-packages (from pylbfgs==0.2.0.3) (1.11.2)
Installing collected packages: pylbfgs, pyyaml, diskcache, pymongo, nvidia-ml-py, pycrypto, psutil
Found existing installation: PyYAML 3.13
Cannot uninstall ‘PyYAML’. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

Same problem. OS: CentOS 7.5.

Hi,

Please see my response here.

Stephan