 people in Moodle. Today we will be installing that FAT++ and R. Yeah, but the stream will be available for two weeks, at least on Twitch, and I will probably highlight the whole stream so that it's saved for eternity. Of course, you can't ask questions at that point. But yeah, of course, the stream will be available on Moodle. It will be here on Twitch, and I will probably put it on my YouTube channel as well, because, and I made a button for that. I need to get a hundred subscribers on YouTube. Otherwise, I can't get my vanity YouTube address. You can see that my YouTube channel is called uciwblahblah, and I want to get youtube.com slash c slash Denny Adams. But you need a hundred subscribers before YouTube actually allows you to have a vanity address. But yeah, definitely, you can do it later. All right, so when you start up Notepad++, Notepad++ looks somewhat like this, and if you would start up R after installing it, it should look somewhat like this. Although this is version 4.02, and I think the newer version is 4.11, but the version doesn't really matter. So all right, I will start in a little bit of audio, just so that we know. And then I actually forgot which buttons I pressed earlier. So it might be that we get the same thing again. So the choices are sunny, too cool, upbeat, happy youth. I think we had youth, which was the one that there was a little bit spooky. But I didn't hear that one myself because I went out. Let's start some happy music. Let me make it a little bit softer so you guys can hear me still when I'm talking. So yeah, first steps. Become an open-source developer. Install Notepad++ when you're on Windows. If you are on Mac, it's called BB Edit. And if you're on Linux, then Linux comes reinstalled with many good text editors. And of course, for Windows, you can just download it. On Linux, it's probably an up-get. And on the same download page, the Mac version should be there as well. Turn off the music, actually. It's really annoying having music in your ears and trying to talk over it. No one's done yet. Like, I can say in chat that I'm done, but really want some feedback here, guys. Sounds a little bit like I'm like, all right. Perfect. Thank you. It's a lot of X's in your name. Done with those two. All right, then continue with the next one. So the next one will be Git. It's the next link in chat. So it's the Git SCM download, which looks like this. Press this button when you're on Windows. So it's just three software tools, which we'll be using during the whole thing. So it's better to install them now. Normally, if we would do this in person, then everyone would be sitting there with their laptop, and I would just be walking around annoying you. Also done with Git. Perfect. Perfect. You're on track, on track. All right, then you can start reading the first, or you can start making your GitHub account then by going to github.com. So just make an account. Oh, yeah, when you do your account, oh, I forgot, I made a slide about that. So Git is something that allows you to collaborate with other people, right? You can visit it there. So it does version control on scripts, and there will be a lecture later about how version control works and the different types of version controls. But do use your how we email again account when you sign up with Git, because it allows you to get the pro version for free. Otherwise, you have to pay like $4 a month for it. But when you are a student or a teacher, you get the pro version for free on GitHub. There's probably some button like I always pay for it because like when I made my GitHub account, there was no such thing as free stuff for people who are in academia. But nowadays, there should be a free pro version that people can use. So the website looks like this, there's just a sign up button. So you just like to sign a button fill in the required information and should be okay. So how about the other people? How about the other students? How are you guys doing? Did everyone was everyone able to install those three little things, except for, of course, Schnei ha ha, because of the fact that they're streaming on a phone, which is perfectly fine, but quiet airtime. That's why I actually have to cricket things. I can just sit here waiting for you guys to answer. Anyway, anyway, guys aren't really talkative. That's a shame. It's much fun, much more fun when people just spout random comments. The Windows computer is unfortunately very slow, so it's going to take some time. Perfect. We have time. We still have 30 minutes for and of course, the rest will be online. I actually put the presentation on mood already. So if you're done with registering your GitHub and you just want to continue, then just look at the presentation online. What the next steps are. Yeah, it's always difficult. People have varying amount of internet and watching Twitch also takes up some of your bandwidth. So it could be that it's so slow. I'm just going to go through the next slide. It's asking how many team members will be working with me. Should I just put just me or more? I would say just you. I haven't made a hit up account in a long time. I have mine for 13 years or something. So when I signed up, it was just fill in your email address, choose a password and go. But how many? No, you don't want to have a team account. You just want to sign up, get the basic account and then get the pro version. But you can fill in that you're probably going to work with a couple of people, but one is perfectly fine. Just say just me. Okay, they're not going to suspend your account if you start working with other people in the future. They're not that mean. They're actually quite good for a company which has been bought by Microsoft, their service is still really good compared to other Microsoft products. So they, yeah, they but they're the kind of one of these. They're one of these. How do you call it? Well, they're not a software provider because they don't provide it right because they're just a website for people working together. So let me actually show you my kid just so that we can actually get an idea. So I'm logged in. Let me move to Firefox. So this is how my kid currently looks. So you can see that, like, this is one of our PhD students who actually starred one of the other repositories. Then this is one of my old bosses, he created two new releases of his more genus AMX software. Scurita is an old student who actually is relatively active on github by looking at other code and doing things. But you can just kind of keep track of what people are doing. So have new versions of software are released. So to give you an overview. On the side here, you see my repositories. So these are the repositories that I'm more or less actively coding in the last time. And then I have I'm a member of two different teams. I'm part of the G network to team and I'm part of the QTL HD team. So I work together with other people, of course, on coding. And that's one of the nice advantages. So the biggest thing that you guys and I think let's just go back to the here. So generating an SSH key. I think that most people that are watching should by now have downloaded the software and installed it. And it's just following the steps on this link. So let me go back to github. No, I can get the link from the chat, of course. So it's just two documents that we have to go through. And put up then show you guys my Firefox. So here's the help file on how to connect with SSH. So probably none of you have an existing SSH key. So you can just say, adding a new SSH key to are generating a new SSH key. And then you don't actually have to add it to the SSA agent when you don't put a password on your key. But so yeah, it's just going through the different steps. So we'll just generate a new key. And if you're unsure, you can check if you already have one. But probably you don't. And then here are the steps that you have to follow. So when you install hit, you get something which is called hit bash. And then you just copy paste the text, of course, without the dollar. So the dollar is something that you don't copy paste. Just as a reminder. And this will then generate a key for you. And of course, you have to use the email that you signed up with github. So that github knows who you are. And it's just a way to kind of get a cryptographically secure way of communicating with their server. So that their server knows who you are. One of the nice advantages of it is that it directly assigns ownership to the stuff that you did. So if you ever run into the issue that someone steals your code in the future, you can actually prove cryptographically that you wrote this code at a certain point in time, which is really, really useful if you want to program in the future, and you get stuck in people stealing your code or these kinds of things. So instead of keeping it secure, you can share your code with the world easily. And on the other hand, also have a have a proof that you made the code at this point in time. So so yeah, it's the first steps. So it's just opening it bash, then doing this. And then it creates an E. So it then tells you that it's generating a key. And then you have to enter a file name to save it, which you can just press enter. Because the C users you dot SSH is perfectly fine. And then you type a secure passphrase, you don't have to I might my key for github doesn't have a passphrase. It's a little bit you could put a passphrase in there, but then you're typing in the passphrase all of the time, unless you also do all of the steps here to start the SSA agent in the background, but on Windows that doesn't work as well as compared to Mac or compared to Linux. So when I'm on Windows, I generally generate a key which doesn't have a passphrase and use that key to show github who I am, of course, you have to be very careful. So with the key, right, don't put it on a USB stick and then lose the USB stick because then other people can pretend to be you, which is an issue if you're working in a team. So anyone already got SSH keys generated in the process off. And I will do the I'll do the cricket sound again, if no one answers just so that we have something, because otherwise I'm just sitting here talking to myself, which I'm actually already doing for two and a half hours. Anyone ran into any issues? No issues? So this might be one of the reasons right to do the assignments in person. So I can just walk through the rows, see how far everyone got and help you directly by taking your mouse. Okay, okay, if you if you get the random art image, that's good. So then you you can find your key somewhere here. So in this PC, C drive users, of course, you have to have your your username, not mine, because I'm called outends, but your username on Windows might be different. And then there's this new folder called dot SSH. And you have to make sure that in Windows, you have it set up to show hidden files and folders. And you also want to show the file extension. So because normally, if you're on Windows, then Windows doesn't show you file extensions of known file types. But yeah, if it gave you this little art thing, then you generated your key and you're all set for the next step. So the next step will be to go to this folder where your key is in. I also put the folder here. If you go there, there should be two files, there's one without an extension. And this is your private key. So your private key is yours. Make a backup of it so that you can save it or restore it when you get a new computer, for example, and never ever share this key with anyone. This file should not be sent out by email or on a use B stick that you are likely to use. Because your computer uses this key, so the one with no extension to sign messages. And these messages are called in GitHub terminology, they call them commits. So they are changes to the code that you are making. And the one with the dot pop extension is the public key. And you can share this with anyone. And people who have the public key can verify that the message that you're sending them is encrypted using your private key. So they they are mathematically related to each other. It's the same way as that cryptographically secure email work. So by having a private key and by having a public key, you can give someone the public key and then send them an email which is encrypted using your private key. And then they can decrypt the message and can read what you are saying to them. While, for example, the NSA or the Russians or the Chinese, they cannot know what you are sending or the Bundes Nachrichten Dienst, right? So if you if you want to be annoying for any of these organizations, then you switch to using encrypted communication directly. Of course, your your computer will do some encryption. But you can always add another of layer of encryption to it. So Xanaxin, did you see two files in this folder? Yes, perfect, perfect, perfect. All right, then the next thing is is to open up your public key using notepad plus plus. And if you open up in the notepad plus plus, then you just see a series of random numbers. Let me open up my private key actually, so that I can show you how it looks. So see users, arenas.ssh. And then we have idrsa.pub. So let me actually show you my notepad window then. So the key just looks somewhat like this, right? So it's a big bunch of letters and symbols and things. And it should at the ending of the key have the email address which you registered to Github with. So in this case, my just my Gmail address. And then the next step to do is take this public key, open up your Github settings, right? So go on on Github, then open up the open up your window, which normally you have like a little symbol here. I actually put my photo here, which is possible. And then you go to settings. And then in settings, there's a section called SSH and GPG keys. And there you can click on new SSH key, which I can actually show you guys as well. So let me open up a Firefox. So here we are on my Github. I can go here and then I can say settings. And then in the settings, there's here SSH and GPG keys. So I can just click on that. And then here you see that I have several keys for different laptops that I have and my web server has one and the university. So and here you can manage the keys. And the nice thing is that you can add multiple keys, right? But here you have the new SSH key button. So if I would do this, then it then it says give it a title. And then here you just paste in the key. This is really, really dark, though. Let me actually go to appearance and go to the light theme. So SSH GPGs, say a new one. And then you can fill in a title so that should be my home PC. And then you can you can put the key here. And then you just say add key. And then the next step is to make sure that everything is set up well and working. So once you copied it in, then you can go to the steps outlined here, which the steps are just to try and connect to github. So it just says that you open up git bash again. And then you say SSH minus T gith at github.com. And then it should say hi, and then the username that you chosen. And then it says you successfully authenticated. But github does not provide shell access because you're not allowed to log into their servers. But at least it gives the key to the server that they are using. And by that, they identify who you are. All right. So anyone having an issue somewhere? Genie88? So it's still downloading? Or did it finish downloading and installing the software by now? It's a little bit of a pain. Like I said, a lot of people are not able to set this up. But I do want you guys to set it up. Computer shutdown completely. After installing or just randomly have to start a new. Well, the download should still be there, right? If you did the downloads correctly. But yeah, it's a little bit involved. And you only have to do it once. So that's the nice thing. Once you have your computer set up, once you have authenticated, then you can just use your computer from then on to work together. Okay, bacon, I created an account already into the next step with the key. Okay, cool. Cool. So we're getting somewhere. So that at the end of the lecture, if we have like three or four new open source programmers, because that's what you need to do, right? If you want to become a famous open source programmer. This is what you do. You have to create a github account, you have to make sure that you have keys. And after that, it's just a matter of finding a project to contribute to, right? You might want to fix your own bug in Firefox. And there's a lot of like fun software out there, which will help you to learn programming as well. Like they like one of my one of the things that I collaborated or collaborated on was the decompiler, which is a programming language. And they have all kinds of little projects where you can earn like $30 for adding a new thing to the compiler. And if you if you are part of if you want to look at source code and find bugs, then you can do that as well. Like most software that you use nowadays, like Linux and Firefox and these, they are all using github to kind of distribute their code and work together. Alright, anyone already able to test it? Xalaxin, you're probably the one that's closest. And it's just a single command, right? Like the whole steps outlined here are a lot. And there's a lot of reading involved. But it's just that's the way that it is, right? Bioinformatics is being able to read these things and execute commands and then figure out how things work. And the help files are actually pretty good nowadays, like 13 years ago, it was a dragon to set up. Because then you had to clone the software compile it yourself. And so in that sense, the world is getting better and better when it comes to open source software and how to develop open source software together. So Stester Souter still here. Daniel, are you still here? Are you setting up hit for yourself? No, Daniel left. Daniel, Daniel, Daniel, well, I have to deal with this. Our problem later in the evening, then you can wait a little bit longer. I copied all the links and going to try later. Maybe it's too stressful for the old lady. Shouldn't be doesn't take that much like hard drive space and stuff. But yeah, having a good computer really helps doing bioinformatics in a way. I could have done it in a different way as well, right? I could have just set up you guys for like our server here and do it all for you guys. But I think that it's good to kind of get your hands dirty a little bit, right? And try to install some of the software. But you don't have to copy all the links. I think the PDF file that I put on Moodle actually has all of the links clickable. So then you can just go through the PDF and click on the links there. It says permission denied when you get to github. This is how I made minus T get at github.com. It doesn't say hi some something it just says permission denied. Alright, then probably something went wrong with either copying in the key or the email address in the key is not the same as the make sure that you open up the public key, right? So the one with the dot pub extension and give that one to hit up. In theory, if you get denied, you can also think there's a troubleshooting page as well. Let me actually look that up. Test your SSH connection. SSH information. It's SSH minus I I think. Alright, so you can do SSH minus V minus T get at github.com. And that will give you a stack trace of. So the minus V means B verbose, right? That will give you like a list of commands that it's trying to do. It might be that it doesn't find the key if you save the key to a different location. So if you saved it, for example, to the C, the C drive directly, then that's gonna be then you have to provide the key. So if you have your key stored on the C drive, you can do SSH minus I for identity file. And then you would say something like C double point slash, and then I key dot pub, for example. So something like this will actually use a key. So you will force it to use one of the keys that you have. But don't worry, like it's just something that I'm trying to set up so that you guys can work together. If it doesn't work, we can always find another way of kind of setting it up. But I do think that struggling through as part of bioinformatics, right? And when I was learning bioinformatics and wanting to use hit it because all the cool kids were using it, then I just had to struggle through. And it's, it's annoying getting permission denied after permission denied. But in the end, once you get it working, you have this air folks elabeness, right, which they call it in German, which feels really good. It's the same as programming. If you program and it doesn't work, and you just get stuck. And when you get it working, like the kind of feeling of joy that you get for getting it working, that generally is the best feeling in the world, because you got it done, you got it done on your own. And of course, again, to everyone watching it now or watching it later, if you really get stuck somewhere and think, I need help, then just contact me and you can, I can invite you to my office here and we can sit behind your laptop together and figure it out. If you're a student and you want to have help and you're using your local computer, which you can't move, then we can always use something like TeamViewer to, like, have me take a look at your computer and see if I can get it to work. So but do do try it yourself. So I'm really, really hoping that at least one or two of you get it working. But like I said, there's no guarantee that it will be okay. The nice thing about having in person lectures is that I can see you guys struggle, which is part of the fun way. As a teacher, it's always nice to see people struggle and then kind of reach their goal and have the, what do you call it, indirect or folks relatedness in a way. So I already told you guys about the mood box upstairs, right? And the fact that you can use it. There's some other funny things that you can do. There are some rewards. So if you subscribe to the channel, then you build up something called channel points. And you can use that to highlight messages and stuff. Because like, you build them up automatically. And if you have enough, you can actually have me do a slide in German, or a slide in Dutch, because I'm originally Dutch. So I speak Dutch and a little bit of German and English, of course. But it's always nice to have like student or have students have the option to have me do a slide in German, because I can't prepare it, right? I don't know which slide you are going to do in German. It's always funny to hear me struggle with German. Xanaxin, still permission denied, still bashing your head against the keyboard. It's like 50% of the time for a bioinformatician. Bioinformatics is hard, man. You don't get anything for free. Yes, yes, still permission denied. All right. Send me a stack tray. So do the ssh-v-tgithatgithub.com and just send it to me by email, then I can see where it goes wrong. It probably will say something like no valid key found or you generated. No, that shouldn't be either. It's difficult. Normally, I would do like I would show you how to do it. But the problem is, is that I can't because then I would just rack my PC by making a new key overriding the old one. And it's a little bit struggling. But struggling is good. Struggling means that you're learning something. And that's the most important part. Like you don't learn stuff by copy pasting stuff and everything going right. That's what people generally think. But that's not the way that it works fortunately. All right, become. Did you get the key generated? Just what you get in the in the terminal, right? Not you don't send me your private or public key. Not yet. All right. Good. Oh, we have time. Like that's why it's homework, right? You have the whole week to kind of figure it out. Not that you should spend the whole week on it, right? Try it for like, half an hour to an hour. If you get stuck, just send me an email, tell me where you got stuck. And then I can hope to make it better. And should I copy and just send all that I get? Yeah, yeah, I'm pretty good at reading stack traces. So we can just look at that then. Yeah, of course, when, when you're almost done, like that's why the slide is almost done with three exclamation marks, because this is a hard part. Once you have it set up, then the next steps will be relatively easy. Sending it to my Gmail or my Hau account thing, start clicking the refresh button on my Hau account. How will mail server can be very slow, can take up to like two or three minutes. Of course, we can listen to some music in the meantime, but like the music isn't that good that you get for free. If it works out well, and the music is not stored in the video on demand later, which I hope it isn't, then we can actually have some real music next time. Alright, let me look at your stack trace. So it doesn't find your key. It has all of these debug one identity file, right, and then it says C users, your username dot SSH. And then it looks for IDRSA IDRSA. And every time it says minus one, which means that the file is not found. No, it actually will attempt key. So it finds the RIDRSA. So it's trying your different private keys. Are you sure you uploaded the dot pub file? And did you open it up with notepad plus plus because it's very important that you don't open it with a standard kind of notepad, the one that is with Windows, because that actually will not show you the proper that that will not it will have like, how do you call it these automatic enters and stuff in there, which Windows loves to do. Yeah. So so what what what kind of a key did you generate? Did you do an IDRSA key? Oh, after open, you have to add it to get it. You did that. So the and then that's my fault. I'm sorry. I'm sorry. So let me show you that again. So you go here to get up, right? So you go to your hit up settings. So the settings box here. And then in the settings, you go to SSH and GPG keys. So on Firefox, right, close the stack overflow question that I was looking at. So here when I go to SSH keys, right, I there's the button here to say new SSH key. So when you go and say new SSH key, you give it a title here, which is something like home PC. And then you just paste the whole thing. So control V, the whole key into the box. So did you do that? And then you click add, then you have to fill in your password again, because when you add a new key, it wants to make sure that you know the password. And that should be okay. It's difficult. It's difficult getting your SSH key to hit up and making sure that you can connect. It's, it's probably, it's harder than writing software, because it's something that you, you have to do like step by step, exactly the way that they want you to, and just adding like just copy pasting it and then accidentally like adding a single additional letter to it will just like not work because cryptographic keys are so you go to your settings, which are here. So you have settings here. And then after settings, click on the SSH and GPG keys, and then say add new, the little add new button, and then just paste the key here. So the public key, not the one with the extension.pub. Okay, done with that. So you now added it here, then try the SSH command again. And now it should say welcome username that you chose. And then that then it should realize that oh, you signed your message. So you signed your authentication message with the private key. Oh, yes. See, our folks are late. That's what we're aiming for. That's what we're aiming for. Good, good, good. All right, perfect. Perfect. All right, that's at least one. So then the next steps. I'm sorry, bacon and genie, genie 88. Maybe it's too stressful for the old lady. Yeah, computers. Yeah, so then the next step is to so you check that and then you just go to my bio info 2021. And then if you go there, then there's a little button called fork. And if you click this little button, it will give you your own version of the code. And there is no code in there. It's just a read me file. But and then like if you click the button, which I can't do of course, because I already have the repository. So show you my Firefox again. So if we go here, right, so this is the bio info one, then here you have fork, right? So when you click this, then I get the option to fork it to one of the two kind of groups that I'm in, which I don't want to do. But normally you would say if you if you go to my bio info 21, then you can click the fork button here, and then you get your own copy of this repository. So then there's two versions, my version and your version, which exists purely online, and then using the command below. So again, in the git bash window, you can make a local copy of it, but make sure that you change any items to your own GitHub username. And then you can do in the git bash, you can say git clone, and then this whole thing with your own username. And then magically, a folder appears, which is called bio info 2021. It's a kind of magic, but it's something that we have to do. So again, anyone that's following the course and doesn't get it to work, don't hesitate at all, just send me an email. And we can either meet in person when you have a laptop, if you want to set it up on your own computer, we can just use something like Team Viewer to kind of get it working. And no problem. I know it's a little bit difficult, like that, that, like, I'm throwing you completely in the deep end. And this is something that generally is like, super advanced. So that like, I do want to stress that that the rest of the assignments are going to be like, a lot easier. It says no such file or directory. All right, so you tried to get clone. You did click the fork button, right? Let me see, you can actually, if you go to my account on GitHub, which is just right, if you do like this, right, then you can have there's a follow button or something. So if you follow me, then I can see what your account is. Yeah, no, you forked it very good. So you have it. So then in theory, this, if you open up hit bash again, right, then saying, let me see if I can, I can clone your version quite easily, actually. All right, so you're almost there then. So let me add a new capture just on top. Right, open up that one. That's very, very dark again. Let me just put it like this, right? Is this readable? Right, so I would generally go to a folder. So I would say, for example, on the on the on the C drive, I am going to say get clone, clone, right? And then you are Sonax in. And then this is your address for your then this is the address for your repository. And then if I do it like this, it would say cloning into blah. And now when I do a dear command, then there should be now a bio info 2021. So it's the if if if you successfully authenticated with github in the first step, then you should be able to do hit clone hit at github.com. And of course, you have to do this from the github bash shell. So the bash window that you get with with github. And yeah, again, it's difficult. So I'm stressing everyone. If you get stuck, send me an email and ask me for help. And I can help you directly. And that's no issue. Because I do know that students tend to not ask for help and want to figure it out themselves, but then spend like three hours on it and then say, well, I'm just going to follow another course. Oh, yeah, sure, you can see the slide. Right. So I know that you click the fork button because I got a message that you made your own copy. And then of course, you just change Danny Adams by your username. And again, this is case sensitive. So you registered your username with a capital X. So you have to use a capital X. Again, like the devil is in the details, little small changes with like, and you could also because if you let me, let me show you the Firefox window. So here's me, right, looking at your repository, right, because you click the fork button. And then here if you click on the code thing, right, it gives you the correct address as well. You have to go to SSH. And here is the so it's hit space clone space and then this whole address. So you can just do right click copy paste. So beacon, did you get a SSH key generated? Or are you still stuck at the SSH key step? Okay, there it works. So you mean you get a folder on your hard drive, which is called like it says that. Okay, so make sure to add the key. So the public key to your hit, right? So so go to your go to your settings. But at least we're getting somewhere, right? Like I wasn't expecting everyone to be done exactly at five because of the step. Jay, all 97. Thank you for following. People should have heard the sound now, I think, like I set it up that there should be some sound for it. Alright, so you have the same problem, right? So make sure and that's, that's, let me show you again. So okay, good. So you can go here, right? Then you go to settings. So go to your own login to hit up go to settings. And then in the settings, you go to SSH and PGP keys. And then you just say here new SSH key, you give it a name, and then you just paste the public key here. So the public key is the one which has the extension dot pub. Like it says, the key begins with SSH and it ends with your email address. So if the email, so the email address that you typed in using key generation, that's the one that should be here. Here is to see how many forks we get before the next lecture. This is the last step. Yes, yes. So the last step is to get the own version. And then there's, well, there's one more step, right? So the step is is that if you, if you open up the local, a local directory, right, then there's one file in there called readme.md. So we, I, the idea is that you make a change to this file, and then push this file to github. So the way that it works is that you open up the file with notepad plus plus, and you add a personal message to the readme, right? So yeah, it worked or something, right? Then you save the file. And you go to git bash, then you type the command git status. Then I made a screenshot of how it looked. So I type first git status, right? Then it says that, oh, there is, it's up to date. So but there is a change, right? So there's not states for commit. And then I just say, okay, so now I want to add the readme, which I updated. Then you say, so this will add the updated readme file, so it will make a change sort of stuff that you typed in. Then we do hit commit minus m and then a message. So in this case, it's updated to readme. And then you do hit push. And then what it will do, it will tell you that there's one file which has changed and there's some insertions or deletions that you made. And then once you push it, then it is pushed to your version of the code. So and I can, I can see that. So when you when you push a change, then it should be possible for me to see that you made a change. And then the next step is to, so this is an example of what happened. So we changed the version has online in your own online version. And then the next step is to submit the changes to me so that I can update my code with your changes. And that is called a pull request. So there's a button called pull request. If you click it, it will then show you the changes between your version and my version. And then you can just say submit pull request. And then I get an email notifying that you made a change. And that's it. That means that you're now an open source developer because you contributed to an open source project, because the code is open source, right? Everyone can read the readme file. And you made a change. So that officially qualifies you as a as an open source developer. So just try it. The four commands is hit status to show if something has changed. And then so yeah, so this part, right? So navigate to where you cloned your local version, go into the folder, there's one file, just open it up, add a personal message, and then issue the following four commands in the grid bash. And then the first command is to see what has changed. So it will tell you that the readme.md is updated. Then the next step is to add the readme. So say I made a change, which I want to keep forever and ever because it's version control. Then you say hit commit minus M. And then you give it a message, say for example, updated to read me or added my own personal message. So this is something that you can choose freely. And then hit push is the way. So you're saying, take my changes and push it to the to the to my remote version to so to my own copy of the code online. I can actually monitor here if you're still not changed. So it's a little bit involved. And like I said, it's not easy. It's not easy being blue, or an open source developer, or a bio information. But it's worth it. It's worth getting to kind of know how these systems work. The message I add is to any part of the document. Yeah, just change anything that you want. Like it's just a readme, right? So you can add just be aware that this is visible for everyone. So don't shout, don't be mean, don't do hateful speech or whatever, right? You're a professional developer. So you don't want to, you don't want to add like horrible messages. There is actually a Twitter bot, which monitors github commits. And if you curse in commits or use other like foul language, it will take your commit message and call you out to the world to say that, well, this guy used the word fuck, which happened to me once. But it was, in my case, it was valid because I added support for programming language called brain fuck. So I use the word fuck in the commit message being added support for brain fuck. And then the bot picked this up and then tweeted it out to the world. Just one by one. So first hit status, it shows you that the readme has changed after you make a change, of course. And then you just say hit at readme.md, press enter. And then it will tell you that the readme has changed. Let me switch to the next slide, right? So here, then it will say that, okay, so you updated the readme and one file changed, two insertions were made. And then you do hit push, and then it tells you, are you in the folder bio info 2020 is the is your is the last part of your URL. If not, then you have to go to the folder because if if you do hit clone, it makes a new folder. So then you have to go into there. And going into a folder is called CD. So change directory, bio info 2021. So you do this command to go into the folder. For God, I should add that to the slide. Let me actually update the slide directly to let me update the slide directly so that the next person Alright, open up the readme. The next is to issue the following commands. So it is here. Go go into the folder, which you can do by CD bio info 2021. And this C is of course small. And I will make this also green. Now that I searched into the folder, it works. Let me see me refresh. Fresh. Alright, so then the status works, and then the other commands should work as well. And once you do hit push, the local or the remote version should be updated. And then I should be able to see that you made a change. And that's it for today, which like we took 55 minutes, which is fine. Like it's it's it's not something which is easy. Like of all the developers that I know, I would say that like half of the people, it's asking me who I am. Oh, because of the it shouldn't actually, that's why we generated the SSH key so that you don't have to do that. That's an interesting. That's interesting. Interesting, interesting, interesting. Alright, so at least I've updated the slide. So let me add this. What do you mean? You don't know you don't know your it's just asking them for your username. But that's strange that it asks you for because when you did the hit. Oh, right. Right, right, right. Thank you, moderator. You have to set your local name because you can actually hide your email address because of privacy reasons if you wanted to. That's true. Let me look that up for you guys. Tell it who you are. Alright, so that's two more commands that you have to execute then. So let me actually update the slide. New slide. Tell it who you are. Alright, so the commands for this are, oh, that's really, really small. Right, so there's two commands which you want to add, which is and then here, of course, this is you have to change it by your username. So let me make that red. Let me make that red. So set your email and username. Can you guess I will copy them to chat for you as well. That worked very poorly. Let me do it in two goes. So just to have this one. And then the other one is and of course, change your name to a more logical name, right? So it's two separate commands. The first gives get your info about the email address that you're using to commit. And the second one is giving a username. And this username doesn't have to be the username of your GitHub account. It's nice when you set it to that. But in theory, you could give it any username that you want, but give it the username that you use for GitHub, of course. So let me update the slides. Right, that's the annoying thing of trying to do stuff when you have it already set up. So these are commands. So they should be in a green. And then this part should be red, because this is your things that you change. Alright, so make sure to change the red parts to your email and your I totally forgot about that. Like that's because you do it once and then you just forget about ever doing it and just you assume that it's set up. The next step would then be to go into the folder to get status at the read me, updated it, push it, and then that should be okay. Alright, let me go to back to reader mode. So yeah, this is then almost there. So we're just I'm just gonna sit here, wait for you, Sonax in to make sure that you finish your connection. And then if we get it working for one person today, I'm going to be very happy. And then we will probably get a lot of emails. And actually, let me save the new version as well. So that I can update the moodle directly as well, replace it, go to moodle where bioinformatics, turn editing on, remove the current lecture, it's with the right. So now I think it worked. This right, let me check. Yes, perfect. Perfect. Adding some example text works with a question mark. And yes, it did. So if you now go to your repository online, right, then it should now show you a different read me. So if I look at yours, then let me check. And here it says that yes, you are one commit ahead of me, because you made a change, right? And if I would go here to the commit, right, then the commit would show that you remove this line and then add it these two lines, which is a little bit strange because you add it just added works. But it worked. So perfect. You're all set up for the next lectures. So a lot of struggling, right? Because over an hour or just over an hour to have one person set it up. So but I'm, I'm happy, like, my job is done. I made a new open source developer today. So that's, that's good. So I'm hoping that during the rest of the week, the other people will struggle through it as well. And in the end, have their own folks relatedness. So if you now wanted me to update my version of the code, right, then you would go and say, pull requests here at the top. So by clicking on pull requests, you then send me a message saying that, oh, I changed something and I want you to incorporate my change as well. But you know what, I am going to give you a, can I still do that? Few rewards. No, I can say that community will say add sin. And I will make you a VIP. So in theory, when you say something now in the chat, you should have a little diamond in front of your name. So applause, applause, like 10 points to Gryffindor, or however you want to call it. Perfect. No, I'm really happy. Like I didn't I, beforehand, I actually expected this to not work at all. Because like, see, perfect. All right, there we go. First new open source software developer. I'm so happy. Like I added this part to the lecture, like two days ago, because I do want to use the collaborative software. Normally, if we do it in person, it's not a big deal, because I can just walk around the computers and just do it for everyone and directly help people. So I was really hoping that it would work like me trying to talk you through it and being supportive would work. But perfect. Alright, awesome. So of course, if you're a student, and you also want to have a little diamond in front of your name, just let me know. I can just put a little diamond in front of your name. Alright, so the only step that I forgot was that one. So thank you also for reminding me that you have to indeed give your username and password to hit up. I totally forgot about that. So because you do it once and then you never do it again. And okay, so this is that and then we added this and I updated online. So I'm not in. Perfect. See you next week. That was it for today. So I think we did quite well. Like in theory, the lecture is four hours, right? Because it's four semester and so you got it done 40 minutes before time. So perfect. Alright, then we had one person more who was still struggling. They come. Are you still here? Are you still struggling? We have Maddie two shoes. Hey, Maddie. I just saw you in the user list. I was checking so welcome. Are you enjoying the show still here? Haha. Okay, cool. Are you still struggling with the key generation? So yeah, I think there the main step is to not forget to add your public key to your settings. That's one of them. The other one. I don't know if they try it for a couple more minutes. I think I will end the stream. Oh, key step is done. Oh, perfect. Oh, wow. Now we're getting somewhere. Then we have two open source developers by the end of the stream. So this work then the SSH minus T. That's perfect if that worked. Very proud of you guys. And then did you already fork it? I'm getting there but slowly. No, trust me, you're way way ahead that like anyone who can fix this within like two hours or two and a half hours is pro. That's that's not slowly like it's it is really hard. I had been programming for more than 10 years before I figured out how to use hit. And then like the tool is so complex that like it's written by the guy who wrote Linux like imagine how complex the tool is. So but no, I'm really proud that we got one person finished. And like, I'm really glad that you're still struggling, right? I'm really glad that you're still here and trying, because it is difficult. And I know that you shouldn't start the first lecture with something so difficult, because you just lose a lot of students that then think like this guy is crazy, I can't do this. But on the other hand, if you start with something difficult, then the rest of the assignments will be just a breeze, right? The next, let me check what the next week assignments are. So next week, the assignments are. So we have phenotypes. I forked it, but it says cannot fork because you own. Okay, but then you're trying to fork your own one. Let me check actually, because then you probably have already forked it. Yep, I see your repository. So if you forked it, perfectly fine, you already have it. So let me show you here in my Firefox window. Right? So this is your own personal branch, right? You see that it's forked from mine, and you are become and you are having your own version. So then the next step is to get it locally. So now because you have so now online, there are actually three versions. So we have my version, we have Xanax's version, and we have your version. So your version is live. So then the next step would be for you is go and let me the PowerPoint. Yeah, so the next step is to get clone. And then of course, use your own username. So let's just open up just get bash again, then say hit clone, and then use your username, which is bacon. It's perfect. Perfect, perfect, perfect. So we're getting somewhere, like I was really wondering if this would work. But like, I'm, I'm so proud of you guys. Really, that's, I think it's amazing. So you're almost done. Although we forgot that there was one additional step, right? So but I was, I was wondering if it would be too hard, because if no one would have like finished at the end, then for me, it would be of course, like, I can't do this. Normally, like in person lectures are easier for kind of this. So we might want to discuss it at the beginning of the next lecture to see if, if anyone like figured it out. Well, we know that two people at least figured out to get the SSH key set up. But it's difficult. It's it's really like, I can't say this enough. Like, let me look at the next week assignment. Like next week assignment for phenotypes is, yeah, next week, we're just going to look at the. So I add Danny Arans and not no, no, you change Danny Arans, right, which is my version by your own username. So in this command, the hit clone command here, you change, oh, you change Danny Arans to pk a n n n, because your username actually has three ends, I think on hit up. Yeah. So in your case, it, the command would be get clone paste. This one. So that would be then your command to clone your version to your local hard drive. No worries. Thank you for sticking with it. Yeah, for anyone still watching the video, because like, I think when people watch it online, it's going to be difficult to follow, right? But if if you're still with us at this point, then next week is going to be really easy, because it's just going to be go to this database, click here, click there. What does it say? So it's it's not going to be make your own super secret key. Is the recording not getting too long? Yeah, the recording is now at one hour 16. So for anyone watching online, I'm just going to close the recording. If you run into any issues, any issues at all, send me an email, set them an appointment, take your laptop with you, and I will help you set it up. If you want to get it set up on your local PC, send me an email, say, I'm home then, and we can sit for 45 minutes to set it up. And then we will just use TeamViewer or something like built in Microsoft thing. But yeah, for everyone watching, I will continue helping make on get it set up so that at least he has one little commit in there so that he has his own air folks elapeness. But yeah, I will see you guys next week. And then this is the end of the recording. So thank you very much for watching. No matter where you're watching it live on Twitch or later on YouTube. It's difficult. I know that next week will be easier. Next week, we will be talking about phenotypes. So thank you very much for watching and see you next time.