Open upendrabhattarai opened 3 years ago
Sorry this is such a pain to use - hopefully there's not much to do to get it working from here.
I think you should just need to move the assembly-stats folder to a different location to get this to work. When you set up the web server on you computer, it is configured to serve files in /Library/WebServer/Documents or /Users/
As you have followed the link in issue10, you should get the message "it works!" when you visit http://localhost. This means that files can be served from /Library/WebServer/Documents, but as this folder is owned by root, you will need to use sudo to move the assembly-stats folder into it. if you do that then your url should look like http://localhost/assembly-stats/assembly-stats.html?path=/assembly-stats/json/&assembly=output&view=circle&altView=cumulative&altView=table.
If you also set up the user site hosting, then visiting http://localhost/~your-username should show a basic web page and you can move the assembly-stats folder to /Users/
If one of these options gets you past the URL not found error, then we can work out how to debug from there.
Hi Richard,
Thanks for your reply. I copied assembly-stats folder to /Library/WebServer/Documents and tried the first link you provided, I got past the URL not found error, and now the page looks like this:
Then, I tried with the test json file for Danaus plexippus and it worked, I could see the circle plot, cumulative, and table:
Now I think web configuration and scripts are working, Thank you for troubleshooting.
I need to work on input file preparation to make it work.
I got the output.json using scripts provided:
perl asm2stats.pl genome_assembly.fa > output.json
and also
perl asm2stats.minmaxgc.pl genome_assembly.fa > output.minmaxgc.json
Both of these json files produced no graphs. Can you please suggest, what can I do to make it work?
Cheers, Upendra
Rename output.json
to output.assembly-stats.json
will do
http://0.0.0.0:8080/assembly-stats.html?path=json/&assembly=output&view=circle&altView=cumulative&altView=table
(I set up with python -m http.server 8080
)
Hi, Thank you for this tool! The graphs look great and I would like to produce them for my genome assembly, however, I am getting the same issue as Upendra. I managed to produce .json files for my assembly with asm2stats.pl and asm2stats.minmaxgc.pl, I set up the web server and I can visualize the .json files provided as examples, but when I try my own files I get the page but no graphs (same as Upendra above). Renaming the output.json to output.assembly-stats.json doesn't change anything.
I will be thankful for any suggestions. Cheers, Aga
Hi, it's exactly the same for me as for @tilia2501. The files are all in the same directory, the names all end in ".assembly-stats.json", they include the same keys (except that Danaus has CEGMA values whereas my file, Heliconius, and Operophtera don't), the latter 3 even have the same line numbers. But still I can visualise the graphs for all the example files but not for my file. I would appreciate any help. Cheers, Saskia
Hi, @swutke, I played around with the .json file and discovered that if I open it in another text editor than gedit and save it back with the .assembly-stats.json extension, it suddenly starts working.. I don't know where the problem is. diff doesn't show any difference between the working and non-working file. Hope this helps! Aga
Thank you for describing what you tried - I've just realised that I updated the example html to require the .assembly-stats.json
, but missed updating the example commands in the README. I think changing the extension should be all that is required. I'll update the README now to use the correct extension
Hi, Thank you for writing this wonderful program. These figures look really nice. However, as I have no knowledge of the java program and being a newbie in bioinformatics. I have not been able to run the program.
What I did was:
assembly-stats
on my home folderoutput.json
usingasm2stats.pl
script and placed it in theassembly-stats/json
folder.But it says The requested URL was not found on this server. I also tried with the test JSON file the same way and it's the same error.
I am also confused with the scripts you provided in
usage
section for where to use.Can you please help me with it?
Thank you, Upendra