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I have checked all the main directories on ftp. Can you tell me exactly where it is? Make sure you are connecting as user gsapubftp-anonymous for downloads. If you connect as user gsapubftp which is for uploads , you will not see the bundle. Thanks for any help.
Ick , I'm not sure what you mean by "no prompt". What program are you using? I'm just using Internet Explorer 8. If I enter the address as ftp: Is there another way I should be doing this? I would recommend using a separate program like FileZilla, which will make it much easier for you to set up and manage your file transfers.
Hi Geraldine, thanks for the explanation. I found the bundle now. I think our confusion came from the fact that until one or two weeks ago one could access the bundle with an internet browser simply by clicking on ftp: Seems like the reference ucsc. It throws an error when I ran the program.
Are you sure it's not your bam that is mis-sorted? That seems the more likely explanation unless you can show us otherwise Hi Eric, does it need to be sorted in the order of 1,2,3,4, X,Y,MT as described in the introduction? No, the official ordering for UCSC is a little different: Hi, I was wondering if there's a way to do this from the command line. I tried ftp but the cluster I'm logged in to doesn't allow it. If you're just using a browser and not FileZilla to download from the FTP site, you can specify the username like this:.
Sure -- just keep in mind that when we update the bundle, you'll want to change the version number, and you might not know you need to do that unless you look at what's in the bundle. It requires that curl, gzip, md5sum and wget are installed. Hi Geraldine, Would it be possible that, in the future, the resource bundle could be made accessible using rsync?
This will shrink that data transfer load when updating That's an interesting idea; we don't have the resources to work on that right now but I'll try to get that on our TODO list of improvements for the future. Can't guarantee when that'll get done though, it could be a while -- that TODO list is already pretty long!
I am sure if you tell your network administrator that you can shrink the network data transfer load, this will climb up your list pretty fast ;-. The idea is to 1 Create a link called "latest" to the bundle's latest version directory 2 gzip the data with the parameter: If the users are interested in versioning, they can make a copy of the bundle files before rsyncing.
Hah, I'm sure it will climb high on the network admin's list; but it's my todo list I'm worried about. Hi there, It's not necessary; anything you upload using the upload-specific login gets put in a directory that only we can take data from.
Anybody else can only browse the directory and see filenames, but they cannot download the files. So your data will be protected. The server has some restrictions on what you can and can't do in a session which aren't under our control. We recommend you simply use a GUI client to access it and you'll be fine.
As mentioned previously, the ftp server doesn't respond well to shell access, so we recommend you simply use a GUI client to access it. Sorry for the inconvenience. I did use the gsapubftp-anonymous username but I don't see a bundle directory.
So I ended up this wget ftp: No, what you want is the bundle directory. It should be at the root of the dir you end up in when you log on. The reason for failed transfers is listed as "Incorrect password". Are there some files there that aren't meant to be downloadable or is something wrong? I selected the failed transfers and shoved them back into queue, second time around they worked.
I can't connect to ftp server. Thanks in advance, cheers! You can download the source and compile: I'm compiling using 'ant' and I have configurated build. Logging in as gsapubftp-anonymous Using a graphical client from my desktop, I seem to be able to download files, but with the above command I get 'permission denied'.
What I am I doing wrong? I'd like to download the larger files directly to our compute cluster so using the graphical client is not a good option for anything except testing.
Unfortunately right now you cannot bypass using a GUI client. This is not under our direct control; I will try to look into a better solution with our IT infrastructure folks but I can't guarantee a solution will be forthcoming. Quick follow-up on your question -- can you confirm that you have write permissions on the destination directory local from which you're opening the connection?
Just want to rule out a client-side error. I can't access the ftp download server. I have tried cyberduck, filezilla, chrome browser, terminal.
At all of themI get the following error. Resolving address of ftp. Connection established, waiting for welcome message Could not connect to server. Doesn't matter if I leave password blank as in the instructions on this site or if I put in my email address. We are experiencing issues with the FTP server. We're in touch with our IT support and trying to get service resumed as quickly as possible. We're very sorry for any inconvenience this may cause you.
Thanks for your patience! I am trying to download hg After it downloads around mb, the connection is closed by sever stating sec idle timeout. I am using filezilla. I have tried multiple time but same issue continues. What could be the problem? The bundle directory holds example fasta files as well as hg19 and hg18 files.
But what are the 'b' directories? They look like the same files as hg19 and hg The b directories contain the Broad versions of the human genome reference.
They're very similar but the chromosome names don't have the "chr" part prepended, and there are a few sequence differences. What's really important is to always use the resources that were generated with the same reference as was used to align your data.
Most of our resources derive from b37 so if you haven't aligned your reads yet I'd recommend using b37, at least if you want to take advantage of our resources. Connection closed by server. File transfer failed Status: Connection closed by server Error: File transfer failed after transferring ,, bytes in seconds. This looks like a firewall issue, I'll ask our IT department to look into it. You may need to consult your own IT support as well, to ask if they can do anything about this part of the error: Hi ashwinipatil , can you try setting your FTP client to active mode?
In Filezilla you can find this setting in the Preferences. The bundle is to be used on this cluster, and I'd like to save a lot of time on down-then-upload the cluster is in a different country from where I am by FTPing directly to BROAD, from the machine I'm ssh'ed into.
It would save me days! Do you think that terminal command "ftp ftp. I get a connection refused. Normal ftp from my own computer using filezilla works fine, of course. We've had reports that terminal FTP does not work for many users.
I first used the GUI tool fetch to log in and browse the FTP directory, then right clicked on the file I wanted and selected "copy fetch address" which gave me the above ftp address with the associated username. Works fine with wget which is a very easy-to-install command line tool.