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
- Yes
- 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?
- Yes
- 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.