help running the program

[upendrabhattarai]

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:

1. I downloaded the repository assembly-stats on my home folder
2. created the input file called output.json using asm2stats.pl script and placed it in the assembly-stats/json folder.
3. Configured web successfully following the link suggested in issue 10
4. I then tried to use this link below to run it in the safari browser. http://localhost/~/assembly-stats/assembly-stats.html?path=/~/assembly-stats/json/&assembly=output&view=circle&altView=cumulative&altView=table

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

[rjchallis]

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//Sites so you will need to place the assembly-stats folder in one of these locations.

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//Sites. then a link similar to the one in issue 10 should work. Looking at it again, I think you will need to add you username directly after the ~, e.g. http://localhost/~your-username/assembly-stats/assembly-stats.html?path=/assembly-stats/json/&assembly=output&view=circle&altView=cumulative&altView=table

If one of these options gets you past the URL not found error, then we can work out how to debug from there.

[upendrabhattarai]

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

[hung-th]

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)

[tilia2501]

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

[swutke]

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

[tilia2501]

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

[rjchallis]

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