Problems when installing Bisque locally

[David Tyemnyák]

Hello,

I am trying to install Bisque system locally on Ubuntu 16.04.5 (LTS), my python => Python: 2.7.12 (DEV).

I am getting an error when installing Bisque locally.

• First of all, I could not access data from bisque mercurial repository on your server. It looks like it is empty? So I downloaded the source code from Bitbucket https://bitbucket.org/CBIucsb/bisque-stable/src/default/
• I have spotted, that in requirements.txt file you have commented URL to you package dependencies (so I have tried to uncomment it - but no success with further installation and command "paver setup server")
• When I try to use command "paver setup server" I got following error: 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 try to fix it by installing manually from here https://pypi.org/project/tgapp-registration/, I got different dependencies errors - two packages depends on one package (but different version))
• I have tried the newest setuptools and even setuptools==3.4.4
• I have also tried the newest pip and pip 1.5.6

I am installing based on instructions from here https://biodev.ece.ucsb.edu/projects/bisque/wiki/InstallationInstructions05

I have tried some advice from this thread https://groups.google.com/forum/#!topic/bisque-bioimage/oYWONyuirQ0 but I was not successful.

I need to run it locally, docker container is fine, but I want to have it running for test purposes and be able to add some new functionality and update it a little bit (as part of my Bachelor's thesis). Afterward, we want to add our own modules, and be able to maintain the system by ourselves.

Any advice, please? Thank you.

David T.

 

[Rahul Vishwakarma]

Hi David,

The instructions below may help you in fixing this issue.

No need to update pip but make sure you have activated the "bqenv" virtualenv 

# Activate Virtualenv

bisque$ source bqenv/bin/activate

I was able to setup this package by commenting the "tgext.registration==0.1dev" line in the requirements.txt file. 

Also you should the package separately as follows

# Install separately since packages may be deprecated in PyPi

easy_install http://biodev.ece.ucsb.edu/binaries/depot/tgext.registration2/tgext.registration2-0.5.2.tar.gz

after this you can run the pip installation again as 

pip install -i https://biodev.ece.ucsb.edu/py/bisque/dev/+simple -r requirements.txt

This should fix your issues.

Regards,

Rahul 

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[David Tyemnyák]

Thank you, it helped. But now, I am facing this error:

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

No matching distribution found for tw.output (from bqserver==0.5.9)

Also I do not have line "tgext.registration==0.1dev" in my requirements.txt. Maybe I do not have the current latest code. I wrote in my previous issue, that I had problems with cloning mercurial repo from Bisque server, so I had to download it from Bitbucket. Any way you could send me the newest code? Maybe it could fix all of my issues.

Thank you very much!

David T.

Dne úterý 13. listopadu 2018 22:45:05 UTC+1 Rahul Vishwakarma napsal(a):

[Rahul Vishwakarma]

Oh, you have the same ubuntu and python version as i have setup on my local dev setup.

You need not clone the code as the following bootstrap py script does it for you. Hope you are using this.

$ mkdir bisque && cd bisque

$ wget http://biodev.ece.ucsb.edu/projects/bisquik/export/tip/bisque-stable/contrib/bootstrap/bisque-bootstrap.py

$ python bisque-bootstrap.py bqenv

Regards,

Rahul

[David Tyemnyák]

Yes, it is working now. I had problems with my virtual machine. Thank you very much!

But now, I am facing a problem with bq-admin setup

I have tried to Install imgcnv manually by downloading (Ubuntu 16.04 image). Maybe something bad is with my settings. See installation log for details.

Any idea? Thank you!

Dne středa 14. listopadu 2018 0:02:12 UTC+1 Rahul Vishwakarma napsal(a):

[satish yadav]

Copy the imgcnv .so files to /usr/local/lib and the executable to /usr/local/bin and then run sudo ldconfig to update your library configuration files. This will solve your problem

[David Tyemnyák]

Like this? It does exactly the same thing. And the .log is the same as before.

Dne středa 14. listopadu 2018 16:58:12 UTC+1 satish yadav napsal(a):

[satish yadav]

Can you share the logs once?

SATISH YADAV

[David Tyemnyák]

Dne středa 14. listopadu 2018 18:52:46 UTC+1 satish yadav napsal(a):

[David Tyemnyák]

It works! Not sure, which package exactly, but I have installed git (it was not installed by default), and ffmpeg for something different, but maybe it helped. Thank you for your advice!

Dne středa 14. listopadu 2018 19:07:39 UTC+1 David Tyemnyák napsal(a):