problem with bisque installation

[Venkata R Edara]

Hello All, 

I am following the bisque installation instructions given here , when i try to configure using paver setup engine, I get the following error saying 

Could not find a version that satisfies the requirement tgext.registration2 (from bqserver==0.5.9) (from versions: )

No matching distribution found for tgext.registration2 (from bqserver==0.5.9)

When i Google the above python package I didn't find anything, even in pip repository also I don't find tgext.registration2. 

I found tgext.registration (0.1dev)     - Turbogears registration extension when i did "pip search tgext".

I am using python 2.7.14 and mac os version is Sierra . Any help would be appreciated. 

--

Regards,
Venkata Ramarao,
visit my site:
techie-builder.blogspot.com

[smart....@gmail.com]

I figured out solution to this, but In next steps I am facing problems.
when i run bq-admin setup. the step 3 in installation instructions, I am getting following error.

./external/feature_extractors.zip No such file or directory. complete log is here.

I am using Mac OS X. I also tried having docker installation, but even the docker images have so many problems and could not install bisque.

(bqenv) venkatas-MacBook-Pro:bisque venkataedara$ bq-admin setup
Developer installation
DIRS: {'bin': '/Users/venkataedara/workspace/bisque/bqenv/bin', 'run': '.', 'share': '.', 'packages': '/Users/venkataedara/workspace/bisque/bqenv/lib/python2.7/site-packages', 'data': './data', 'virtualenv': '/Users/venkataedara/workspace/bisque/bqenv', 'default': './config-defaults', 'jslocation': 'bqcore', 'modules': './modules', 'depot': './external', 'config': './config', 'public': './public'}
Developer installation
DIRS: {'bin': '/Users/venkataedara/workspace/bisque/bqenv/bin', 'run': '.', 'share': '.', 'packages': '/Users/venkataedara/workspace/bisque/bqenv/lib/python2.7/site-packages', 'data': './data', 'virtualenv': '/Users/venkataedara/workspace/bisque/bqenv', 'default': './config-defaults', 'jslocation': 'bqcore', 'modules': './modules', 'depot': './external', 'config': './config', 'public': './public'}
This is the main installer for Bisque

The system will initialize and be ready for use after a succesfull
setup has completed.

Several questions must be answered to complete the install. Each
question is presented with default in brackets []. Pressing
<enter> means that you are accepting the default value. You may
request more information by responding with single '?' and then <enter>.

For example:
What is postal abbreviation of Alaska [AK]?

The default answer is AK and is chosen by simply entering <enter>


Beginning install of ['bisque', 'engine'] with ['server']
CALLING <function install_external_binaries at 0x10626db18>
Fetch external binary files from Bisque development server [Y]?
Matched section Darwin-64bit-*
extjs.zip found locally
bioformats-pack.zip found locally
ImarisConvert.tar.gz found locally
CALLING <function install_dependencies at 0x10626dc80>
No pre-compiled version of imgcnv exists for your system
Please visit biodev.ece.ucsb.edu/projects/imgcnv
or visit our mailing list https://groups.google.com/forum/#!forum/bisque-bioimage
for help
ImarisConvert is up to date
No pre-compiled version of openslide exists for your system
Please visit our mailing list https://groups.google.com/forum/#!forum/bisque-bioimage for help
Bioformats is up to date
CALLING <function install_features at 0x10626ded8>
Install feature extractors (Feature Server) [Y]?
Unpacking ./external/feature_extractors.zip into ./bqfeature/bq
An Unknown exception occured [Errno 2] No such file or directory: './external/feature_extractors.zip'
During setup:
Exception:
Traceback (most recent call last):

File "/Users/venkataedara/workspace/bisque/bqcore/bq/setup/bisque_setup.py", line 2983, in setup
r = bisque_installer(options, args)

File "/Users/venkataedara/workspace/bisque/bqcore/bq/setup/bisque_setup.py", line 2797, in bisque_installer
params, runtime_params = step (params, runtime_params)

File "/Users/venkataedara/workspace/bisque/bqcore/bq/setup/bisque_setup.py", line 2312, in install_features
uncompress_dependencies (filename_zip, filename_dest, filename_check)

File "/Users/venkataedara/workspace/bisque/bqcore/bq/setup/bisque_setup.py", line 2144, in uncompress_dependencies
if tarfile.is_tarfile(archive):

File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.py", line 2624, in is_tarfile
t = open(name)

File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.py", line 1675, in open
return func(name, "r", fileobj, **kwargs)

File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.py", line 1740, in gzopen
fileobj = gzip.GzipFile(name, mode, compresslevel, fileobj)

File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 94, in __init__
fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')

IOError: [Errno 2] No such file or directory: './external/feature_extractors.zip'

[pndal...@gmail.com]

Unfortunately, BisQue is not really supported for anything but LInux (that documents/web-page is way out of
date) and you will find numerous problems building your own system which is why we recommend the
Docker images. The file that is missing, for example, is feature_extractors.zip (which I could send you) but it
is Linux specific:

% unzip -vl feature_extractors.zip
Archive:  feature_extractors.zip
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
       0  Stored        0   0% 2013-10-04 17:14 00000000  src/
       0  Stored        0   0% 2013-10-04 17:14 00000000  src/extractors/
       0  Stored        0   0% 2013-10-04 17:14 00000000  src/extractors/MPEG7Flex/
       0  Stored        0   0% 2014-04-30 16:26 00000000  src/extractors/MPEG7Flex/lib/
  582211  Defl:N   234120  60% 2014-04-15 15:25 4f556dd8  src/extractors/MPEG7Flex/lib/_MPEG7FlexLib.so
       0  Stored        0   0% 2013-10-04 17:14 00000000  src/extractors/VRL/
       0  Stored        0   0% 2014-04-30 16:27 00000000  src/extractors/VRL/lib/
  168847  Defl:N    39269  77% 2014-04-15 15:25 418ebdd5  src/extractors/VRL/lib/_VRLLib.so
       0  Stored        0   0% 2013-10-04 17:14 00000000  src/extractors/WNDCharm/
       0  Stored        0   0% 2014-04-30 16:27 00000000  src/extractors/WNDCharm/lib/
 1783885  Defl:N   392987  78% 2014-04-15 15:26 6a39b8d3  src/extractors/WNDCharm/lib/_WNDCharmLib.so

As you can see it contains Linux shared libraries (.so) and not Mac OSX compliant ones (.dylib).

I have not tried the Docker images from Mac OSX but will. You can also install an Ubuntu system under
VirtualBox and run the Docker images from there.

[pndal...@gmail.com]

Note that I can run the docker image from Mac OSX:

% docker pull cbiucsb/bisque05:dev
% docker run -p 9898:8080 cbiucsb/bisque05:dev

then point a browser to localhost:9898 and login with admin/admin (or create a local account).

I do not seem to be able to run the stable one, though!
P

[Venkata R Edara]

Thanks for your help, i also used fedora Linux but the docker container is not working on stable bisque version. Do i need to use only dev version?

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[pndal...@gmail.com]

On Fedora Linux have you tried running the docker command under sudo?

 % sudo docker run -p 9898:8080 cbiucsb/bisque05:stable

If that fails, yes use the dev version.
P.