 Welcome everybody. My name is Saskia Hilteman and in this video I will walk you through understanding the galaxy history system. So we have a nice tutorial on this topic. You can find it in the topic Using Galaxy and Managing Your Data, which you can find from the home page of the GTN. Once you scroll down past these scientific topics, you have these galaxy tips and tricks. And if you click on this topic, you see that we have a lot of topics about the galaxy interface itself, about uploading data, histories, workflows, you name it. So today we're going to run through the basics of the galaxy history system real quick. Different releases of galaxy, how the history system works may be slightly different and how it looks. So this one was recorded on version 2301. And I will walk you through the changes here. Okay, so you see here your familiar galaxy with the tools on the left are a working panel in the center and our history on the right. You can see that I have already added some data sets to this history. So every item in your history represents a file. They are numbered just an order that they were added to the history. And you can name them. Let's start with naming our history so whenever we have a history. We call it, they'll be called unnamed history. But it's a good idea to always find a good name for your history. So we're just going to call this something like example history. And then to save it, there's this button at the bottom. And you see it changed that. Now you probably noticed that there were some more options here. So let's hit this pencil icon again. And so we can also add some tags, for example. So if you want a little bit more information that maybe you can't all capture in the title, you can add here. Anything you want to remember about this history. So maybe the project it was for or the data set you analyzed. So you can choose here from anything you've used before. You can type something new. So let me say something like project a you can add as many tags as you want. So you can say cohort 17, anything that you want to remember. And if you want to remove tags, you can just hit this little X icon like that. If you want a little bit more detailed information, you can also use this annotation box. So here you can really sort of describe in a couple of paragraphs, what he did in this history so you can say this history contains analysis of well, whatever you did in that history. So this thing here is that if you share this history with other people or if you publish it on Galaxy, this will be visible too so it's really a description of what you did that if you want to share or publish. And we're going to hit save again. Okay. So you see also here some extra information about the history so you see here the size this current history is four megabytes, these two files. So if you're in the state of galaxy you also see your quota how much you are using so I have plenty of space left, but if this number is getting close to 100. You might want to look into your histories, find large ones that you don't need anymore and delete them. So let's see for a sec tagging we did annotating three size. So if you add, if you run jobs if you, or add data sets by the upload they will appear here. They're green now so that means everything went okay with creating the data sets. But if you run a job, you may see some other colors. So when you first start a job, your data sets will be great that means galaxy knows this file will be created but it's still waiting for the job to actually run. And when the job is running it turns orange like this. And then when it's finished it turns either green or red if there was an error. And it can also be pause that means that like there wasn't an error with a previous data set that this job is dependent on. So this is pause now until you resolve that error. Okay, so each of these data sets in your history also has a couple options so if you click on that it will be expanded. You can see some information so this is a bed file with file with chromosome locations and galaxy knows a little bit about this this file format so it can tell us some information. You can see a number of regions that are in this file, for example, you can see that you can also add tags to data sets. Again, if you want to remember anything about this. And if you put a hashtag in front, and this will, this tag will also live with the data set so if you run any jobs on this data set those resulting data sets will also have this tag. There's a nice tutorial specifically about this and how you can use it to better manage your analysis. So you see here that without expanding you have the icon that will show you the contents of the file in the middle. You have also this pencil icon. Okay, there it goes it loads. They can see really the contents of the file. You click on this pencil icon can edit the attributes so you can also change the name here to make this a little bit more more informative so let's say repeats on chroma so 22 just be a little bit more specific for example. You can add a reference genome here so if you for example have a BAM file that was aligned against specific reference genome. You can choose that here and galaxy can use this information in some of the tools in order to use the right reference again. So we can save that again with the save button. You can see the name was updated here. Now you can also delete data sets from your history with this delete button. So now it's gone from my history so you can do that if you added a file by accident or if this went wrong and you're trying to keep your history clean. This icon up here also appeared. So this is tells me that there's one active data set in my history and one deleted one. So if I want to still see the deleted one because it wasn't actually removed yet. It's just deleted from my data set and and I can still view the file and edit it and if I want to undelete it I can click this and delete button and I'll come back into my history. We see now that by clicking on that rubber spin icon I filtered up here my data sets for deleted is true. So now I can clear that filter again to show everything. And this box can be used for any sort of searching so I can say, let's say I have 100 files in my history, and I don't want to scroll to find the one but I know I remember that I called it exons you can say here exons, and it will filter for anything that matches. There's some more advanced searches you can do here so they are listed also in this tutorial. So let us go there so you can also really specifically tag search for example for a certain file extension. So you can say extension VCF. Nothing there bed. Okay, because these are both bed files it'll find it. So if you're looking for specific data set in a large history, the search option is very useful. And now there are also things that you can do. So you may have already encountered collections in galaxy. So this is really if you have a large number of samples, and you want to run an analysis on this entire batch of samples at once. So if you don't want to run the tool manually free everyone of them. You can make a collection, and certain ways that you can do that is using this sort of this checkbox to manage multiple data sets at once. And here you can select files from your history that you want to apply an action to. So use the select all button if you want to do it for everything. And then there are multiple options here if you click on this all to select it. You can do sort of bulk operation so you can hide all of them you can delete all of them. You can leave all of them permanently so then there's no longer an undelete button, and you can build a collection. Or tags to all of them at once things like that so that's really nice if you need to do repeat the same operation on many different data sets in your history. So let's say I want to turn this into a data set list a collection. Then that is the option and you can give here a name for your collection bed files for example, create collection. So those two files have been replaced with this one collection. We can exit this selection mode again by clicking on the checkbox again. So now you see for example that we have one history item, which behind the scenes, both of these files that we had. So you may create as many histories as you want and it's advised that you create a new history for every analysis that you do. So then if you want to switch back and forth between histories are multiple things you can do. So at the top here these arrow buttons will show you a list of your histories in order of when you last updated them, and then you can switch to a different history. So I have a couple that I've used before, and then if I click on this, it'll change my active history and load that one. And then I'll just going to change back here. Now there may also want the times where you want to compare histories. So if you go to this. See didn't switch it. Let's do that. Oh wait, no, I'm clicking the wrong button. I want to go back to the example history. There we go. So load this one again. So if you want to sort of compare to history side by side, and maybe move some files between them, you can do that here. So we have this little drop down menu for history options. This used to be the gear button. So you see that I have in total 40 histories. You can copy a history as well. So if you want just a copy of the history in its current state. And before you for example try some experimental analysis you can do that. You can also delete the entire history so if you want to get rid of it free up some space. You can do that. You can extract a workflow from your history again we have the better tutorials I'll deal with that. So here are the nice things you can do and yes you can share this history with other people or with everyone on the galaxy server. Let's have a look at this show history side by side because it's quite useful. So here it'll show your current history. And then you can select any other histories you want to also display so here there's nothing displayed yet. I'm going to click on the select histories. Let's say we want to compare it again with this other history. So this is just a really a random history that I already had, but here you can see and you do as many as you want. Let's add this one. I'm going to compare these side by side, but one nice thing you can also do is you can drag here. Data sets between history so if I let's say I want to have this file that I used in this other history for analysis if I want to also have that in this history. I can just drag it over like that, and it will be copied. I have set copy to history to my history, and I can start using it. So this is definitely a lot better than re-uploading the file again because now there's only one copy and you don't have any duplicated data as you save some space. And now if you want to hide this again you can say hide or directly from this menu you can also switch to this history. Now for this history that I had, you may have seen this icon that we didn't have before. So files can also be hidden. This is just to keep your history a little bit clean, but you still want to keep the data, you just want to show it by default. So this often happens when you run workflows and they can be configured to only show the most important outputs of a tool and hide some of the intermediary data. But if you do want to look at these files, you can click on this button. You see here that created this visible equals false filter. And then we can see here everything that has been hidden for this history and you can also unhide things here again. It's a little bit different than deleting, but also very useful. So now if we want to show our normal view again we can clear this search filter. Okay, so let's say we want to delete this workflow. So we go to the history options again, we can say delete the history, I mean, workflow, say confirm. But anything in Galaxy when you delete it, it's not so maybe retrieved again. So if that was a mistake, it might still be around. So if you want to check this, you can go to the user menu at the top and view all your histories in this way. And now you get a little bit different view, but you can some more advanced searches here. So you can search again for names and tags in this advanced search, you can also look for your deleted histories, and you still get a chance to undelete them. Or you can purge them forever. So if you really want to clean up that space to clean up more space disk space, you have to delete them first and then click here to delete permanently to get that space back. If it was mistaken can always still undelete it. Okay, I think these are the basic things you need to know about the history, you have this refresh button that shows you when those last refresh so if you have that internet connection maybe this hasn't been refreshed recently and then you can also manually hit this button so if your data sets are turned in green for example, double check that. Okay, so with that I think you know the basics. There is a little bit more information in this tutorial if you want to see it and the rest you'll probably pick up during other tutorials. So thank you for watching and enjoy.