There are several places that you can upload files in PATRIC. You can upload them using the upload monitor that you can see down here at the bottom right of the page. You can upload them within the app, we will take out here and upload it. Or you can upload it from within your workspace. Let's start with uploading from the workspace. So you click on the Workspace tab at the top of the page and then click on Home. This will give you access to your workspace where you can see all the data that you have there. This is mine, what a mess. I have used PATRIC for a long time and this just shows what a cluttered person I am. And I don't want to contribute to the clutter that you see here. I don't want to reform myself and create a folder for reads that I want to upload. So I'm going to show you the right way, don't follow my example. Let's create a file that we want to upload data to. So up here in this upper right corner, I'm going to click on Add Folder. This will open up a pop up window that allows me to name the folder that I want to `put the data in. We'll just call it My Reads, so I'm going to create that folder. And you see here, there message pops up that shows me the folder has been successfully created. Now, I have to find it in my shame of how messy my workspace is, can be seen by all. So once I get to My Reads, I click on this icon, folder icon here. And this shows me the folder is currently empty. So I want to upload some reads here. I'm going to click on the upload icon in the upper right. This will open a pop-up window, and look here, Upload type. We want to upload reads, well, I mean, depending upon what you want to do. But this is a precursor to assembly, so I would want to upload reads. But if you click on this down arrow, you can see all the different things that you can tag the file type with. It's important because these are the things that PATRIC itself can read when it's within a different service app to try to figure out what you want to do. So I want to look for reads that I'm going to upload, so I'll click on Reads. And it gives me a message, and it tells me that I need to find files that are structured this way. An important message is that Genbank formatted files are not currently accepted. So it's restricting to these type of file, switch or FASTQ files, FASTA files or gzip files, or bz2 files. So let's click on this blue Select Ffiles button, and I actually want to go into downloads, I have some files there. Let's click here for this file, and I can only do one at a time, and click Open. And I can see the file here in these are my reads files, and I'll say start upload. Now, this is a big file, and nothing's happening here. But if I look at the outload monitor here, it's showing me that it's starting the upload. Important to keep track of this, it's showing me the file and what it's uploading to my PATRIC workspace. And you don't want to launch any job until this thing has been 100% complete uploaded. If you launch a job prior to that, the jobs going to fail, be sure to monitor the upload. Now, if you're working remotely, you can't leave, you wait until it's uploaded before you do anything. That's just to say that sometimes we have people with unstable Internet connections or they close their computer in the middle of an upload. That's not going to work very well. So while this is uploading, and you can see it's a big file, it's taking some time. going to leave this window open, and you can see it's starting here, but it's got the size of 0, so it's going to take awhile till we see 100%. So if I go into services here, and as soon as we were going to do assembly, let's click on that. Let's say you wanted to upload files within this server. Yes, I would need to click on this folder icon here or here. If they're single reads or pair greens. Let's click on this and I can go down and find that folder again to say I want to upload it into this specific folder. My reads folder and look it's telling me it's already uploading this one. I want to upload a new one. And look, when you're within the Pacific Service it's going to automatically tag a file for what you want, which is reads. It's the assembly service only sees reads. I say, select that file and we wearing downloads an now I'm going to get the make paired to it and select open here and here is the second one. I hope that's the second one. I hope I didn't, it's like the same one twice and it's starting the upload. Now look, it's telling me that now it's uploading a different one and this is currently up. See it's starting to tick up, but you notice that the name is present here, so it's uploading it here. Now there's a third place that one can do uploads on, and let's go back to this workspace to see where we're at on this. So this one is still only at 82%, but these are big files and it's taking awhile to upload them. And this is the R2. And then when I go over to this tab. You can see I'm uploading its paired read and that's only at 11%. But both of them eventually will appear in the workspace. Right now we're at 90%. Now another place that you can do uploads is right here from the upload monitor. So if I click on this icon here, it will give me a pop up window that it won't allow me to drill into my workspace. It's just going to put it in my home directory. And this is one of the reasons why my workspace is so cluttered 'cause they haven't gone in and cleaned it up. But it's pretty much the same thing you click on this and it'll get into the home directory. Now let's say I uploaded some data an I had it marked as unspecified. If it's marked as unspecified, the Assembly app can't see it. So I'm going to show you what that looks like, so I'm going to click cancel here. And while this is uploading because I already have this in my workspace, I don't care so much about it. I'm going to go into here to my home directory going to show you how you can change the tag on some data. So if I click on this folder here you can see here beyond the green bar where it says type, it's unspecified. I uploaded this, the read files that I can see from the fast Q, but Patrick doesn't know they are read files. It's an unspecified file type. So when I'm within the app service for assembly, it's not going to be able to see it. So I need to re tag this. See this down arrow click here, and it re-formats the box. I'm not sure why it does that, but anyhow, it looks better here. Now click this down arrow and let's click read because these are reads and then save. Now it will be tagged as reads and everything's going to be okay. You can see the app service can see this. Before we sign off let's see how this is going. Sometimes it takes a little bit of time. It says here that we have 100% of the reads. Uploaded, but sometimes you need to refresh your page to actually see it. Sometimes it'll take a few minutes before it shows that they are the correct size in that they've uploaded correctly. Let me repeat once more do not launch a job with these things that they have not been completely uploaded. It will only bring you sorrow and pain. So those are three ways that you can upload files into Patric. Through the workspace. Through the upload monitor. And through the app itself, going here. Now let's go onto assembly. Are you ready for your first assembly assignment? This has two parts. One, within your home directory you need to create a folder in your workspace. This is the folder where you're going to put your reads and the assembly jobs. Now within this folder you could have folders within folders within folders. But first let's just create the first folder. Then you can structure it however you want. Now within that folder I want you to upload the following MOOC_test One ASCII reads and MOOC_test_2. These are paradon reads that I'm going to ask you to assemble at some point. So where are those things? You go into Workspaces and click on that upper tab and then it will show you all the workspaces. The workspace you create will be in your home directory, but the reads are in the Public Workspaces, so you click on that. This rewrites the page to show you all the workspaces that are in the public workspace. And Patric, click on the MOOC Patricc Course. It's good to click on the globe there. And then you click on that and you'll see an assembly folder within that. You click on the assembly folder, and within that you'll find the two pair of reads. So what you'll need to do is select them both by Shift click, and then notice that when you do this the vertical green bar has the possible downstream function, it's only going to have one which is the copy icon. So it's going to copy this data from the public workspace to your private one. You click on that, and then it'll open up a dialogue box with your homework space. So you would click on the homework space and drill down to the folder you just created and store. You'll copy the data there by clicking OK when you're done so, good luck. Let me know if you have any problems. Bye.
