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Issue with visualization #12
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The In addition, you need to create routes and views via the https://github.com/neherlab/pan-genome-visualization/blob/master/add-new-pages.py |
Hi Richard, Thanks a lot for your answer. I seem to be still lost. I am using this command: /Users/pablovargas/pan-genome-analysis/link-to-server.py -s /Users/pablovargas/pan-genome-analysis/data/TestSet -v /Users/pablovargas/pan-genome-analysis/pan-genome-visualization The TestSet folder contains all the output from a pan-genome-analysis run. and the argument for -v is the location of the pan-genome-visualization folder. However, there seems to be an error because I get this when I run the command: rsync: link_stat "/Users/pablovargas/pan-genome-analysis/pan-genome-visualization/./data//Users/pablovargas/pan-genome-analysis/data/TestSet/vis/." failed: No such file or directory (2) Then I check my localhost server http://localhost:8000/ and cannot find my data. Do you have any idea what I am doing wrong?????? Thanks a lot for your help. Cheers, |
The problem is that the |
Hi Richard,
I am very sorry to bother you again but I still cannot make it work. I have
followed your indications and those from the pan-genome-visualization
GitHub website and it is just not working for me.
This is what I do, sequentially,
1. Open the terminal
2. cd to pan-genome-analysis and then cd to pan-genome-visualization
3. Run the bash file > bash add-new-pages-repo.sh TestSet
4. cd to pan-genome-analysis and run the python file > python
link-to-server.py -s TestSet -v
/Users/pablovargas/pan-genome-analysis/pan-genome-visualization
5. cd to pan-genome-visualization
6. Run the command > npm start
7. Go to my local server and then check if I can find the entry TestSet
but I cannot find it.
I have checked that the TestSet directory is located in
pan-genome-analysis/pan-genome-visualiation/public/dataset/ and that all
the permissions to all the files in the TestSet directory are in order,
i.e. I changed all the files permissions with chmod 777.
I am running all this process in a Mac terminal. Please let me know if
there is anything other detail you would need from me. I really want to
make this work. I find your pipeline very complete and would like to try it
on a real set of genomes I have.
Thank you very much in advance.
Best regards,
Pablo
…On Sun, Dec 9, 2018 at 5:41 PM Richard Neher ***@***.***> wrote:
The problem is that the -s flag is only supposed to be the name of your
run, i.e. TestSet in your case. cd into
/Users/pablovargas/pan-genome-analysis and then execute
./link-to-server.py -s TestSet -v
/Users/pablovargas/pan-genome-analysis/pan-genome-visualization
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Same problem here ! |
Please check the following:
The latter two are created from the |
Works for me now. |
that's weird. check which file the browser is actually requesting (and hit ctrl-U to check the exact path of the script -- somewhere at the bottom). |
when you open the file in your browser and it doesn't exist, you'll the the server's error page which is html. |
So I know this is not the GitHub repository for the pan-genome-visualization package but I am super lost regarding how to make the visualization work.
What exactly are the arguments to be used for the link-to-server.py script???? I understand that argument -s needs to be the folder containing the files from the output of pan-genome-analysis. However, I do not know what the argument should be for -v. I have tried the absolute path of the pan-genome-visualization package, the relative path of the local host server 800, but to no avail.
Could you please help me out with this one? Thanks in advance.
Cheers,
Pablo
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