I have recently configured a local instance of the Galaxy 17.01 software on a CentOS 6.9 server, and have got the service running enough that I can login as the administrative user I've defined and install software from a remote Tool Shed. However, whenever I attempt to upload a .bed file through the web GUI, it appears to be uploading fine and then ends with the status "Failed: Bad Request (400)". I've tried a number of different files and types including those from examples online, all of which give me the same status. The files are only a few KBs in size, so are by no means too large to upload through the web GUI, and in fact, I can upload them in the usegalaxy.org web GUI without issue.
I assume that I must have a misconfiguration somewhere that I need to resolve, but strangely, nothing is showing up in the galaxy.log file beyond the HTTP POST and the error code 400. There is no additional information to go on, so I'm at a loss where to look.
Any help that anyone can provide to help me debug this issue would be greatly appreciated!
Please let me know what other information I can provide to help in this process as well.
For the 400 error, this usually indicates a web browser issue. Chrome, Firefox, and Safari are recommended. Try clearing your browser cache and then uploading again.
Samtools should be installed in order to upload and work with BAM/SAM datasets, so make sure that has been done. Also, you might have problems with certain tool installs with Galaxy version 17.01. Some changes occurred since then with respect to how tool dependencies are managed. Upgrading to the latest Galaxy version is strongly recommended.
Release notes: https://docs.galaxyproject.org/en/master/releases/index.html
Let us know if this does not resolve the problem,
Thanks, Jen, Galaxy team
Thank you for your response Jennifer! I have installed the 17.05 branch of the Galaxy Git repository now with a fresh install and am using Google Chrome as my browser, which has been updated to the latest version available. I've cleared my cache and downloaded the package samtools version 0.1.19 from the Tool Shed. I am getting exactly the same results, it says that I have made a Bad Request (400) and no additional information about why it won't accept any uploaded data.
Please forgive me as I'm brand new to Galaxy and don't really know all of the "knobs" to turn in the configuration file to get more verbose logging or why this error would be happening as I have confirmed I can write to the directory that it should be placing user files. Is there a default set of tools that everyone should install as an administrator before trying to upload files?
Additionally, I can see that after I have started an upload, a new file appears in database/tmp with the correct number of bytes, current timestamp, and correct data inside. So it appears that it is properly writing the data to the temporary file location, but is failing to transfer that data into the user files?
Thank you in advance for your help!
The Samtools package is not enough, the actual tools need to be installed (the package that contains the repository dependencies would be installed when the suite is installed, example
However, the most current version of Samtools is recommended (version 2.0.1). There have been changes to the way dependencies are installed (through conda) and various bug fixes, allowing Galaxy to make use of the tools without other admin manipulations (specifically, adding Samtools to your $PATH).
Samtools 2.0.1 has not yet been bundled into a suite (but it is planned for near term). However, the individual tools can be installed and are needed for upload of BAM/SAM data and any manipulations that make use of those datatypes. Perhaps give this a try and test load a BAM/SAM dataset?
Also, to clarify, are other datatypes are still failing upload now when using Galaxy 17.05? If so, let us know. Meanwhile, I will recruit some help from our development team for further troubleshooting.
I've got suite_samtools_1_2 installed on my server as well now, but I'm still having no luck uploading the bed file. I've also tried uploading a .fasta file but get exactly the same result. Things show up in database/tmp but I get the Bad Request (400) error.
Here are the files that I have been trying to load into my instance just for reference: http://bx.psu.edu/~clements/Events/GMOD2013/m.vannielli.TFBs.bed http://bx.psu.edu/~clements/Events/GMOD2013/m.vannielli.sequence.fasta http://bx.psu.edu/~clements/Events/GMOD2013/m.vannielli.wholegene.bed
Do you have any files that you think should work that you could provide to me for testing purposes to confirm that this is a more general problem in my instance than perhaps a few bad files?
Ok, I see the problem. Entering multiple URLs with a direct copy/paste in a single upload query is presenting a problem with the error you state. Exactly why for this case is not clear yet (more testing Monday).
How the problem manifests:
HTTP Error 400: Bad Request
Samtools is still needed to handle BAM/SAM data uploads (and other manipulations), but that is a secondary troubleshooting item.
Have you configured a proxy server by any chance? That could complicate uploading. Otherwise the upload should just work out of the box.
I'm going to directly to the port 8080 site that is being run via the Python paster script, so it should be as default a setup as possible. I plan to go through the Apache proxy configuration in the future, but have not done so yet.