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wurmlab / sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
https://sequenceserver.com
GNU Affero General Public License v3.0
268 stars 111 forks source link

New/Clean install doesn't work #755

Closed wolfgangrumpf closed 2 months ago

wolfgangrumpf commented 2 months ago

I just installed the latest version of sequence server on a new linux machine and when I tried to start it up I got this error:

/var/lib/gems/3.2.0/gems/sequenceserver-3.1.0/lib/sequenceserver/server.rb:25:in `start': uninitialized constant Rack::Handler (NameError)

      @server.mount '/', Rack::Handler::WEBrick, app
                             ^^^^^^^^^
    from /var/lib/gems/3.2.0/gems/sequenceserver-3.1.0/lib/sequenceserver/server.rb:9:in `run'
    from /var/lib/gems/3.2.0/gems/sequenceserver-3.1.0/lib/sequenceserver.rb:122:in `run'
    from /var/lib/gems/3.2.0/gems/sequenceserver-3.1.0/bin/sequenceserver:417:in `block (2 levels) in <top (required)>'
    from /var/lib/gems/3.2.0/gems/slop-3.6.0/lib/slop.rb:260:in `parse!'
    from /var/lib/gems/3.2.0/gems/slop-3.6.0/lib/slop.rb:65:in `parse!'
    from /var/lib/gems/3.2.0/gems/sequenceserver-3.1.0/bin/sequenceserver:48:in `<top (required)>'
    from /usr/local/bin/sequenceserver:25:in `load'
    from /usr/local/bin/sequenceserver:25:in `<main>'
yannickwurm commented 2 months ago

Hmm - was this with gem install?

wolfgangrumpf commented 2 months ago

Yes, the standard (non-Docker) install.

tadast commented 2 months ago

@wolfgangrumpf if you know how to do that, could you please try checking out the branch #756 and letting me know if it works?

While I'm unable to replicate this locally, I think I know what the issue is and we should be able to release a new gem version with the fix tomorrow.

wolfgangrumpf commented 2 months ago

Sorry, I'm going to reopen this since I'm not sure if this is separate: the install moves forward now and sequenceserver launches (browser window opens), but there is no database selection option. Error from the command line says:

wolfgang@Genomancer:~$ sequenceserver /var/lib/gems/3.2.0/gems/sequenceserver-3.1.1/lib/sequenceserver/sequence.rb:235: warning: character class has '-' without escape: /\A[a-zA-Z0-9-_.:*#|[]]+\z/ [2024-07-02 15:26:34] INFO Reading configuration file: /home/wolfgang/.sequenceserver.conf. ** SequenceServer is ready. Go to http://localhost:4567 in your browser and start BLASTing! To share your setup, try one of the following addresses. These may only work within your home, office, or university network.

wolfgangrumpf commented 2 months ago

@tadast

tadast commented 2 months ago

Sorry, the error message is not very helpful, but it seems you don't have blast installed in the system or it's not in the PATH environment variable. 

$ whereis blastn
blastn: /opt/homebrew/bin/blastn

I think some of the changes we've introduced recently might be expecting blast to be installed before we run the setup process. We'll look into this later this week, but if you could install blast 2.15.0+ in the system it should work.

wolfgangrumpf commented 2 months ago

I thought I had taken care of that (I had the blast that sequenceserver downloaded, and I made sure the .conf file pointed at it).

I'll take another look at it tomorrow - thanks!!!!

On Tue, Jul 2, 2024 at 4:13 PM Tadas Tamošauskas @.***> wrote:

Sorry, the error message is not very helpful, but it seems you don't have blast installed in the system or it's not in the PATH environment variable.

$ whereis blastn blastn: /opt/homebrew/bin/blastn

I think some of the changes we've introduced recently might be expecting blast to be installed before we run the setup process. We'll look into this later this week, but if you could install blast https://www.ncbi.nlm.nih.gov/books/NBK569861/ 2.15.0+ in the system it should work.

— Reply to this email directly, view it on GitHub https://github.com/wurmlab/sequenceserver/issues/755#issuecomment-2204307973, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTCZBVA2QEF2EZM65YGNTZKMCYBAVCNFSM6AAAAABKGFTKGKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBUGMYDOOJXGM . You are receiving this because you were mentioned.Message ID: @.***>

-- Cheers,

Wolfgang

Dr. Wolfgang Rumpf Professor, UMUC Computational Biologist, The Research Institute at Nationwide Children's Hospital

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wolfgangrumpf commented 2 months ago

It was a stupid $PATH error on my part. Working beautifully now - thanks for all of your help!