I am encountering an issue on the usegalaxy.org server with the following:
The wigToBigWig tool does not work correctly for my ChIP-seq data, but my boss suggested that the convert bedGraph to bigWig tool works fine for similar data. However, I cannot find the convert bedGraph to bigWig tool in my Galaxy account, while my boss can access it in hers on the same server.
I found convert bedgraph to bigwig tool in the .eu server and finished my work by uploading data to .eu server, use the tool, download and upload the product file to .org to do the following process, but this is really painful since uploading to .eu in US is extremely slow.
Could you please assist in resolving these issues:
Help me access the convert bedGraph to bigWig tool.
Investigate the problem with the wigToBigWig tool, as it is not functioning properly for my dataset.
All accounts at the same server have access to the same set of tools.
These are the two are you interested in, yes? I found these by searching the tool panel with “bigwig”. Once you also find the tool, you can favorite it to put it into a short list just for your account to make it easier to find the tool you use the most faster next time.
Now, to help with your question about a failure, we’d like for you to generate and post back a share link to the history with the job you have a question about. Make sure the input dataset is there, and the outputs are there (from the tool that either didn’t work or didn’t produce the expected result). If the tool didn’t error, you can add in screenshots about what is going wrong.
(sharing this way protects your privacy, just shares your data, makes sure we are all looking at the same data, and you can unshare after. You can even copy just those few datasets involved – the inputs and outputs – into a new history and share that to limit what is seen publicly. Copies of exact data in your own account do not take up any extra space!).
You shouldn’t need to move back and forth between servers for this, but if you ever do really need to move data between servers, that can be done directly without a download step. So, maybe for next time (you shouldn’t need it for what you are doing now since I hope we can help you!).
Thank you for your detailed response! Really appreciate your effort providing me such a lot of information and protect my private info.
Following your link, I can open that “Convert” tool in my .org account, however, I tried using this account to convert my bedgraph file which I successfully converted in .eu server with its “Convert” tool, and it comes with an error saying that " Couldn’t open /corral4/main/objects/8/d/a/dataset_8da1330d-f0ea-40db-9ef8-6c8774217ad8.dat".
What could possibly be the reason for this? If you need further details, I can follow your instruction provided and share the history with the files.
Glad that helps, and yes I would need to see the data to learn the exact reason for your failure. You are welcome to generate and post back a shared link to your history.
If you want to double check yourself, common reasons for failures with this tool are:
Not assigning a database key – either native to the server or a custom key that you create (specific to the server and your account at that server)
Not trimming overhanging coordinates – use the advanced option Clip chromosome positions with the wigToBigWig tool.
Potentially an input that is too large to process at the ORG server. The EU server’s clusters scale in a different way and can sometimes process the largest datasets. The solution for this is to work at the EU server.
to put it into a short list just for your account to make it easier to find the tool you use the most faster next time.