Hey, welcome to Arizona Deliverance Center Wow I've gone through hell and a handbasket in the last six or eight months and bad things happen To people all the time They happen for a reason Yeah, and so here's the way I do it. I asked the Lord to heal me. I go down my list you know I go Is it a repentance thing? Is it a deliverance thing? Is it something I'm not seeing or is this a learning experience Go down the list nothing works bang. You got to go through it Went through that gallbladder surgery remember that one The day I went in for surgery the doctor said hey these gallbladder surgeries are a slam dunk There's nothing to We didn't cut you open anymore.    I got this is fantastic We never surgery every week everything went wrong that surgery It's an hospital for 12 days Oh just six weeks ago. I go in to see the doctor. Hey, you got some bone spurs in your hip here. No problem These surgeries are a slam dunk It was deja vu all over again There's nothing to it. He said some people are walking the next day. He said walking the next day. Yeah So I go to my calendar and I go I'm just going to cancel out of counseling appointments for a week. That's all I need to do Because this surgery like this one is a slam dunk. There's nothing to it. Yeah Yeah, I went through the surgery lasted about 45 minutes I get back to the recovery room I'm laying there and I go hmm. I can't feel my legs So I start moving my feet back and forth in bed there Hey, I'm moving. I don't have any pain. They're right. I'm going right back to work. This is No problem. Oh Yeah, I got discharged the same day. I went home That afternoon Yes, I Got in bed got up to get out of bed to go to the bathroom And started screaming in pain For two days. I'm screaming The third day I figured out how to roll over to the side of the bed Flop my leg over both legs push myself up Grab the walker shuffle off like chest or on gunsmo To the bathroom walker up to the toilet two weeks of the walker Then I got on the cane these surgeries are a slam dunk There's nothing to And I said, hey, I can't take this anymore. I'm about 95 back I said, I got to get out of this house I got to get back to work I'm standing right here Yeah, hey sometimes you got to take it take it the hard way why he does that I think it's patience I think it's endurance. I think it's a learning experience. That's all it is And hey, whatever I got to do and whatever I got to learn to get into the revival that's coming I'll go ahead and do it Fine with me ready to rumble I got a good bible study for you tonight. I hope I'm really glad to be back all right There's the radio programs same hours same days every day of the week actually still on Still on the internet every day all the time you get the archive radios programs there Dark sky radio. That's a secular internet radio station. I had 38,000 listeners last week So that's going pretty good. I'm on every night nine o'clock You can help us with the ministry if you buy something from amazon You just put in our charity name and go to smile amazon not the regular one amazon And they'll donate to our ministry if you buy something tonight's teaches known house of healing az youtube channel live If you know somebody wants to get delivered, they're too afraid to come for help Send me an email mic at hardcore christianity.com I'll send you the two miracle lists one for troubled christians and one for mentally ill christians Okay, you can go to the website and make a donation if you like we get a lot of donations on the website Let me stop right there Both times I've been out the donations went up So I took that as a sign from god Just steady the course I got the thing covered So if I'm not here and the donations go up, I checked with the ministry staff, you know, anyone up It's actually better if I don't show up Everything ran smooth here the thursday nights are booming I get all kinds of reports of people getting delivered and healed Peter has been going hot guns here friday night. Thank god for him So The way I set this thing up is exactly what I just said It's not a me oriented ministry I do my part and I like to let other people work in the ministry and let's see them grow and develop It's not all about me And thank god I did that because when I'm not knowing I was going to be out a couple of times Hey, you want the thing to run well when you're gone You know It's not about me. It's a holy ghost And he showed up here every service everything went great Nobody needs me around here And the donations went up Now when I'm back, I guess the donations would go down But they keep coming in and they've been coming in so well Everything we own is paid off now. It's a deliverance center. There's no debt The healing house next door All paid off. That's no debt Everything's paid off. Thanks to you and thanks to my Friends on the internet. God love you for sending in all the donations All of us here including my wife Work for free I don't take I don't take a salary I'm not in this for the money. I'm in this for God helping people And that's it. Okay I'm not one of these rotten gut TV preachers who's trying to get a mansion and a limousine and Then a homing glory on top of that. No, you homie don't play that All right, so thank you for what you've done Thank you for what you've done Well, the deliverance rival hits here next year the or 2021 whenever it's going to land You're going to be seeing stuff you ain't going to believe Good things that are going to blow your mind The holy ghost is going to Run wild You go on a rampage The devil just it's a slaughter. It's a wholesale slaughter And I was promised a revival I got confirmation of it six times. It's going to happen Okay, there's no question about it If I was you and hang around If you don't hang around, I love you. God bless you I'm going to hang around if I have to come here in a wheelchair and get drug in here I'm gonna Thank you for your donation. All right. I wrote three books.  It's going great I'll be on talk america radio nationwide on saturday january 20th My last gig there was canceled. My host got sick He was in the hospital the same time I was so this is catching Anyway, they rebooted me to june 20th. All right I'll be down at the teen challenge again In tusan in september Thank you for your donations My bible studies are evolving around what the king james bible and we sell this bible here in The bookstore if I were you I would read These five bibles because these bibles are Based on the uh received the text If you read other bibles They're gonna have verses missing out of the bibles Sections missing these will not they'll have all the Verses there and the best translation of the greek new testament. I've ever seen is the one we sell that kj3 bible That's the best one The king james is one I like but it's hard to read because it has a lot of strange old english Uh phraseology in it. I happen to like the bees and dials But I'm old But it is harder to read. Okay, the king new king james is better They took out that part, but they left the good parts in so Um, I'm not telling you to do this. I'm just saying these are just my thoughts All right, let's get into our bible study. It's a political season and as you know America is a democracy And Some countries are not a democracy. For example Saudi Arabia is a monarchy The a royal family Sets up here And runs the country in america This is a democracy every person Theoretically is the same value as the other person You have one vote.  You have a vote. You've got one. You've got one. You've got one It's there, right? Yeah in a dictatorship No, there's one person at the top and he Controls the rest You got a monarchy You got a dictatorship Total control and you got a democracy us What religions in those countries Reflect what kind of a country it is In america christianity is based on a democracy That's why christianity in america Stinks A democracy Ruins christianity Here's the definition of democracy, right? It's a group controls how The system works Everybody votes everybody inside They have a board meeting and they decide where the country the company's going to go There may be 25 people on your board. There may be 15 on your board all major corporations have a board of directors They have a ceo a cfo and so on But the board of directors Controls the corporation correct That's in a that's similar to a democracy a monarchy You have a monarch or a monarch family at the head of the country making all the major decisions of the country A dictatorship is run absolutely controlled by One person or two people And they run the country as they see fit Valenzuela Probably falls in this category Correct, let's take a look at galatians And see how damaging a democracy is for christianity Paul writes in the letter and he says you foolish Galatian who? Pascino That means to kind of put a spell on somebody where they're utterly amazed They're stunned with amazement Wow Kind of like watch Steph Curry hit a three-pointer with no time on the clock How do you do that? Everybody stand there? God amazing. It's kind of like watching a magician magician or a levitation show Goodness sakes. That's amazing. Paul says who bewitched you who put a spell on you That uh, you should not obey the truth Before whose eyes jesus christ was evidently set before you Prografo means that it was paul wrote numerous letters and texts And made numerous sermons and statements explaining the old testament to the galatians Showing them without question. Jesus christ was a messiah He had all the documentation there laid it out like a second grader and hand spoon fed it to him There was no way they could misunderstand That's what he's saying here What happened there?  Let's make a decision here. Let's vote on who we want to go with shall we go with the Which doctor that came in or shall we go with? The word of god Paul says you ran well who hindered you from not obeying the truth. What happened they voted In as only in a democracy to go with the other guy The other preacher the other minister The other messianic do whoever it was that came in This persuasion did not come of god Don't you know that a little leaven leavens the whole lumb How do you get a little leaven in well in christianity christianity is a monarchy Not a democracy All the Information the knowledge the wisdom the commandments the orders come from The royal family who runs christianity here in america. We don't do that We get the information from the royal family and then we evaluated To determine whether or not that information is appropriately applied to us Then we vote on it Well the galatians did the same thing what happened Oh They went to hell on a handbasket.  Why don't know if that's right? I'm not sure we ought to do that That doesn't seem right. Hmm. That bothers me in a monarchy You just simply do what you're told Oh, that didn't go over well in the democracy See america don't like that See americans We have the highest standard of living in the world for a general population here. Okay Now you're rich people. Yeah, there's a big debate over that. There's some people rich in dubai that you know Wall Street guys are going man Guys calm down and you've gone too far But the general population This is the wealthiest country in the middle class here Much better than sudan Valenzuela mexico And name a place How do we get that way? Well, it's a democracy. We all got a vote So when we get saved out of a democracy, we're already implanted by demons Into this lifestyle It's a democracy. It's not it's a monarchy The holy ghost says do this I'm supposed to say yes without even questioning The Galatians started to debate stuff. What do you think? What do you think? What do you think? What do you think? What do you think? What do you think? I think we're screwed As soon as you leave a monarchy and go back to a democracy as soon as your opinion matters Trouble starts to brew in your spiritual life Check it out king saw Got orders from god didn't he first Samuel chapter 15? Hey, just go there and utterly destroy them I I remember what they did to the israelites when they came out of Egypt He says wipe out everything and when you get there wipe out everything you don't take anything back with you It's all cursed now That's it That came from Yahweh or Jehovah And he runs a monarchy. He's the boss So when he tells somebody to do something It's not something's questioned That's what we'll do. It doesn't matter if you understand It doesn't matter if you like it You heard Jehovah tell you what to do And because you know him you know, he's already evaluated it and you don't need to evaluate He already assessed the problem looked at all the alternatives looked at the positives and negatives came to a conclusion and you as a Monarchist are saying what'd you say? That's what we'll do You don't even question Paul says oh, that's what I'll do. This is a monarchy. Yes. I'll do exactly that Guess what happened? uh-oh Uh-oh Saul went from a monarchy to a democracy the people They took a vote Here's what they said shall we destroy everything here? Kill everyone and get rid of everything like Jehovah said let's take a vote Saul raises his hand. Yes, let's do it. Nobody else raised their hand Oh, let's take another vote. Shall we take the good spoils and leave the rotten spoils for Jehovah? Let's take a vote on that. Oh There goes the Jews. They're all voting. Hey, I'm over here. I get the vote Saul goes. Hmm. Looks like the eyes have it We'll take the good spoil and we'll leave the crap And destroy that for Jehovah anybody following this The people voted see that They voted See you don't vote in a monarchy Later on Samuel explains it to me and he says I have sinned. Why did I sin because I feared the people? Hey, he feared the people and Saul did such a good job He was picked out by God individually separately He sent a prophet To Saul's family. He said I want that person. Can you imagine that? God never did that to me I never had God leave the throne in heaven and come down and say Mike Mike you I was no That never happened. I never I've never seen God I haven't oh Mike's my Mike's not very spiritual The Holy Ghost Convicted me of my sin. I never saw anybody I fell someone I fell down At that altar years ago. I fell down I never saw anybody God never blew any trumpets or spoke to me. He went and God saw he said go go annoy Saul king And Saul did a great job. He said, okay, I'll go there. We'll destroy everybody. He he took the place apart And what happened then he flipped back to voting He voted He was out voted And I feared the people So I gave them What they voted for they wanted these spoils here And we we slaughtered this See they skimmed like they were running a casino And what happened to king Saul?  It was horrible. You know committing suicide peter Let's see how he handled the democracy versus a monarchy. Here's acts chapter five check this out They get arrested by the jews. They get whipped.  You had the high priest here Then you had all the other priests, right? And they all got together in a group with gamiel and all the other bible scholars and they all made decisions in a group situation Not peter No Peter was told by god. Listen. I want you to evangelize these people Go get them. I'll be with you. Peter went and got them Big revival breaks out in Jerusalem. They get caught and whipped and beat and cursed and they cut sent back out And they said uh What are you doing?  This wasn't a democracy Had you got that years ago, you'd be a completely different person right now You'd be a totally there you'd be a spiritual bombshell everywhere you went Yes, you'd be a stone cold killer. Why because god spoke to you and whether you understood it or not you just did Why because you know this isn't a democracy I don't vote around here I don't get a group of people around to determine whether or not we ought to keep spoils or not I was told not to keep the spoils. I don't know why I was told not to keep them I don't care why I was told not to keep them. I'm not keeping I was told not to do it Christianity is not a democracy In america, we think it is We go to whatever church we want. We read whatever bible we want. If this bible has got six chapters missing, that's fine. It's all good See we flip the tv Oh, there's a crook. There's a creep. There's a pervert. There's a priest with a kid. Oh, there we just float around on tv We do what we want we vote We run our own show Wow, that's not good What did peter do here Jesus got in the boat he teach he gives us incredulous teaching Christ the teacher the one and only he's finished. He gets out the boat Simons mesmerized by the teaching He's a fisherman. He's got to go back to work and they go float back out to the water and they start fishing They can't catch anything He says hey launch out over here You're you're putting your net over here. Jesus yells any put it over there Didn't explain anything see in a monarchy The ruler explains stuff only when he chooses to explain it If he doesn't choose to explain it it doesn't matter to you you do it anyway period Launch your net out over there Peter He says the teacher we've been fishing all night We haven't caught anything see In a monarchy it doesn't matter what your circumstances are you just do it Peter looked around the boat and the other fishermen were there. He said good.  This is nuts We've been fishing all night But you know what after that teaching after hearing that teaching This this person has got something nobody else has got I just heard that teaching I'll tell you one never the less Because you told me to do it Even though it makes no sense to me Makes no sense to me.    So should you.   Oh, I know man I don't know. I can't you don't know what they did to me. It doesn't listen This is not a democracy and i'm not going to sit here with you and vote on whether you ought to pray for your Child abusing psycho dad You were told to pray for him Whether you like it or understand it or not. This is not Up for a vote. You're on america. Oh, no the megachurch. We vote on everything Nevertheless at your word. He says I don't understand it But i'll throw those nets over there No What happened there a great multitude of fish The their nets were breaking see You see if you'll just obey whether you get it or not whether you understand it or not Whether you like it or not if you will do The right thing because he told you to do it and for no other reason if you'll do that you will experience the one that unto him who is able To make all grace abound unto you Now unto him who is able to do exceedingly and abundantly above All you can think or ask That isn't happening to you your christian life is terrible.  You are told to do it So just do it Sounds like a title of a bible study There are so many fish they yell to the other You see if you'll just do it God will not only supply your needs But everybody else you care about God's blessings bleed off you Onto all the others The other guys in the boat who he didn't say that to who were peter's friends They went home with nothing but fish Why because one person didn't vote They filled both ships There's so many fish the fish began to sink What's going on with this story? Oh, I know Jesus has a fish fetish No, he's trying to illustrate a spiritual principle of the abundance of blessing that comes from obeying Even though you don't understand why he said it I know what you're thinking brother mike. You never met my spouse Come on guys Yeah, how many men are married here?  And you're you don't understand one word The one thing makes sense Karen went home, right? My wife went home I don't understand anything she's saying I got a master's degree I'm lost Experience multiple wives have left me in this position just do it When I was younger with the other wives I didn't have that deep insight just do it If you will obey god when you don't understand him All the blessings will fill your boat and the other boats will fill too Jesus opened his ministry with that other story. Did you know that that was at the beginning of his ministry fish What was at the end of his ministry? Fish Yeah, Jesus loved fish I don't know why I I'm fine with fish, but I don't think about him much But back then Fishing was a great teaching tool It's not now but back then it was This is at the end of his ministry in john chapter 21 Jesus pops up on the shore after his resurrection The other one was in the beginning of his ministry He first started he was teaching in the boat Here he's at the end. He says he's standing on the shoreline. He yells out to him. They're in the boat fishing Peter had a big fishing business And he starts yelling at him he says You got any you got any food the greek word for meat there? Abramo which means food. They said no, we haven't caught anything He said well, listen cast out to the right side of the ship.  Yeah, let me talk to you When you're fishing lord Fish are in the water Okay, they don't care Whether they're on the left side of the boat Or the right side of the boat lord See, you don't know anything about fishing You know about miracles and stuff. You don't fish That's not a fishing story. It's an obedient story The fish were under the water. They were all It's not about where the fish were Jesus said you're on the left side of the boat Throw it over to the right. He was testing you to see if you would listen and obey without Voting Peter Does what? He obeys another miraculous haul Of fish Well, one of the other disciples says hey, wait a minute here That looks like the lord yelling over there Well, peter jumps in the water and swims in and gets the net and pulls it out, right? The other disciples had to come from the other ship About 140 feet away What's a cubit? Do we have any Noah's Ark people here? All right. Well, listen a cubit is here to here See and you can imagine they had a lot of equipment back then it was built in a little way because A cubit with my cubits differ in yours Unlike we have now we got a foot a meter. It's all Penciled out, right? Well, so I said this is about a hundred and forty See, I don't actually know peter dives in and he's dragging the net Too sure there's so many fish Right the other disciples have to help him And guess what? The story wasn't about fishing It wasn't about catching fish Jesus didn't even need the fish He had already provided for them Before they had caught one they come to shore And there's the buffet already there What was he doing there? He was testing the disciples to see if they were under a monarchy or a democracy If you'll obey God And just do it You'll find that your needs are already on the shore Cooking and ready to eat See your heavenly father knows what you need Before you ask You know bring up the fish you caught What kind of fish were these these weren't the fish like the other catch? No These were the big ones Listen, if you will get out of your democracy and start obeying God You're going to get all kinds of little fish as your blessings But as you keep listening and obeying and growing As you get down the road spiritually You're going to get the big fish of the ministry Jesus didn't give them miracles of fish anymore They were he gave them a big one Why nobody voted they were told Throw it on the right side That doesn't make any sense To throw it over there. I could have caught him on the left side What are you talking about? It wasn't about fishing.  You want that you want God's big fish You want the big blessings from God You want not just help here and there. You're looking for destiny You'll never find it by living in a democracy Taking a vote and drawing straws. No, it's not going to happen when you're told to do something You don't even ask why you just do it. Remember that story in Wigglesworth? You stand in there and 3,000 people there They're out in a field They had no microphones on He cries out to the Lord with tears in his eyes. What am I going to do? Help me or 3,000 people there. I can't pray for 3,000 people What do I do? The Lord whispers to him Tell that woman to stand on that stump there that sick woman He tells that woman go stand on that sick without a hesitation Never asked why didn't need an explanation Didn't want to go through it Didn't ask anything about the woman. Can she get up there? Will she get up there? What should I do? He just did it Now tell everybody to look to her and those who look over there in the name of Jesus. They will be healed Hundreds of people Healed instantly looking at that woman standing on a stump Would any of anybody gotten healed that day? No Had he lived in a democracy Well have a woman's old standing on the stump Let me talk to these other two pastors and see what they think about maybe how are we going to hoist her up? Or what if good about Wigglesworth heard and just did it Never asked why? Didn't care why?  Yeah, this doesn't sound like a good teaching, but it is See if you'll obey God and not sit around and question and take votes You'll suddenly hear him yelling at you come and dying I already had your plate over here the jobs already over here the money's already over here the blessings are already over here I was just waiting to see if you'd throw the net on the right side of the boat When this verse sunk in years ago, I changed my behavior. I stopped yelling at God when I was in prayer I figure if I had a problem and yell loud enough, I did Wow, I never knew he already had the coals burning The fish were on the coals the bread was there I didn't even know it That's I stopped yelling Yes, sir Why can God do exceedingly abundantly above? What you're able to think or ask Because you didn't think about what you were told to do you didn't ask a bunch of nauseating questions You were told to do it and you just did it So the dunamis supernatural power within each born-again christian the holy ghost Manifested the miracle. How about this lady? Let's check her out. Was this a democracy or a monarchy?  You know me, right? She says, you know, you knew my husband, right? Yes, you knew he was a good man, right? And he was a faithful servant. Yes The guy died.  It doesn't say why he died and it doesn't matter And I'm not asking why he died the poor guy was gone for some reason and he says jojoba The creditors are coming to my house because We got no money left We got no money. We can't pay our bills the rents do the utilities are being shut off We're getting evicted all these bad things are happening and we have I don't have anything left But my two sons to go into bondage for working as house house servants and various slaves type jobs that they had in those days They were going to come and get the two boys So then her husband's dead And she's home alone After they take the two sons So she comes to Elijah the prophet the man of God and asks for help He says what do you want me do for you? And she said I don't have anything in the house.  I'm finished. It's over. I'm screwed. It's done I'm beaten. There's nothing here We're broke. We ain't got nothing. Elijah doesn't even turn the hair. I didn't even flinch He hears from God and he says what what's he tell her to do?  Is this democracy? Geez. Hold on Elijah Let me let me get my sons here. Do you think we should do this right now? First of all Will our neighbors want us to knock on the door and bother them? Maybe they don't have any pots. Let's figure out who wants to No No No, she didn't ask any more questions She didn't vote on it She didn't get advice from some crook on tv She said we'll go get the pots A this makes no sense whatsoever B that the guy appears to be a complete crack pot What i'm broke they're coming to get my sons and you told me to go to the neighbors to get some pots What are you nuts? See you'll be a powerful man of God someday Superpowered woman of God when you obey God and you don't even ask why She walked out of there Without taking a vote. She didn't ask her sons. She didn't ask her neighbor.  The prophet of God says Don't don't get a few of them get a whole bunch of This message has got to be sinking into one or two people here. It's got to be One or two people will leave here with a changed life They're not going to vote anymore Yeah I'm voting anymore If I'm told to do it By God, I'm doing it period and I'm not asking why Set all these vessels aside and fill them all up with that little pot.  Is that all you got left?  They got all the pots they could Find in that area Here and there ain't no more pots. We're out of pots Some of you were pot heads After the pots ran out. Guess what happened? The oil in that in her pot Disappeared well, she could have developed a Costco there, but let's look at what are really important. She saved her two two sons lives and guess what? Guess what if you'll do what god tells you to do And stop analyzing it To see if that's a good idea or not or see if you ought to do it or not or see if it seems reasonable or not Or is that intelligent or not? Hmm. Let me think about it.   It's all the oil I got left I ain't got any oil either You can have my pots Who walks off the whole story sounds asinine? You don't get it. It's not the point of the story. The point is Did you listen and obey? Well, let me decide about when you stop doing that And you hear god tell you just do it. Hey, you're gonna be a pot addict Oh the powerful general from syria, this is a good one, isn't it second kings five. Yes, sir Naaman Gets a word from his wife They had this young girl who was jewish Naaman was a super powered hero, you know like an avenger But he was different than an avenger in that he had leprosy So he was a sick avenger He was a powerful man in syria People had parades for this guy People got his autographed. He was a Incredible warrior He was Above everybody in the whole country except the king this guy was on top of the world He was dying of leprosy a little jewish girl goes to his wife and says hey There's a there's a prophet in israel that can handle this leprosy thing Go down there Go down and see him And get this thing fixed So the wife comes to the general and she says hey, there's a prophet down in israel you go down there You get your leprosy cured. He goes. Well, that's great. I'm gonna do that Yeah, I'm gonna saddle up my soldiers and my Mules I'm gonna take all kinds of money and give him See this guy's got to be a tv preacher We'll bring him all kinds of gold and silver and cash and he'll let us right in the dough He says a It'll be a spectacular event.  Then he's gonna come over to me and wave wands over me and boom I'll be healed on my leprosy. It's gonna be great. There'll be a parade and everything Well, let's see what actually happened And I'm bang some He comes to see elisha and He don't even come out to meet the guy why Because the guy's arrogant He's a narcissist. He's a avenger. He's a big shot. He thinks he's got all the answers He didn't know at all. He's a great man. He's an accomplished man. He's a respected man. He's earned respect Everybody is serious respect they have parades when he comes in Town and he's destroyed another nation This guy is A big deal He doesn't even answer the door He sends a servant to talk to him What was the servant that gave him the information in the first place? No, that should have sunk him a servant then comes to the door When he gets all the way down to Leisha's house several days drop several days on the donkey He has a long trip. He says hey Where's the elisha when he's busy? He told me to give you a message. What? Yeah, go down to the jordan river Jordan river that place stinks Doesn't matter go down to jordan river Dive in there seven times On the seventh trip out of the river You'll be cured He pulls out of he goes back on heroin. He freaks. Yeah, you nuts God almighty, where's the parade? Where's the king of israel? What happened? I'm talking to another servant He means he's so mad. He can't even see straight. But listen carefully His servant comes to anybody seeing a trail here another servant comes to him the big shot Hey, listen Even you mind if I talk to you for a minute, sir Great one glorious one. May I be heard may I speak just for a moment? Humble myself and be a servant may I serve? May I make a recommendation? okay, he didn't come out with a parade And call lightning down from heaven and give you a rainbow and Angels floating around like a prophetic service. Oh the angels are on the scene Okay, that didn't happen I get it but What do we got to lose? I mean We came here all this way anyway We're already here see You didn't see chevy chase when he went to walley's world.  It's full of mud and stinking stench There's better rivers at home. I'll just go you see He thought it was He's voting He's a voter He's thinking oh, wait a minute. That doesn't make any sense. I've got a superior intellect here. I'm really smart I I'm thinking about this. Yeah, the river's better there. Yeah, we're going back there anyway. Let me dump.  You're going to start getting pissed off And after a little bit more time when nothing happens, you're going to fly into rages When you fly into a rage when you get mad at god You can't think straight anymore Man All of a sudden nothing makes sense anymore Amen cracked man. He lost it He lost it man egos An ego will cause you cause you to lose it your ego.  It's so bad. It's like it's like it's like being filled with feces The ego of god is the sickest thing you've ever seen in your life All the great holy ghost preachers men or women Had dispensed with ego years ago The holy ghost can't use somebody with a big ego He walks right away from him. He passes right over. I've seen it in a man time As soon as you start thinking you're a big shot and you need to evaluate these things and collate them Debate them and then get some advice from others and then make a discussion on it You've lost your miracle. You can kiss that thing about What happens the servants came doing the servants saw him The jewish girl She goes to them the wife See He was such a big shot. She didn't go to him directly But she cared so she went in the back door Knowing that the wife had access to him It wasn't the wife that accomplished it. It was the servant of god The servant answered the door The servant told namen Hey Why don't you just do it? What do we got to lose? He starts to think about it.  You don't understand. You're the you're the main theme you in this story It's not namen. It's not the king. It's not the prophet. It's it's us We are servants of god. We have laid our ego aside and serve others Namen calms down. Oh, dude Listen to me christian.  You'll lose it all What do you do?   You know the story the angels come to sonam and gamora And Abraham goes and oh, it's a lord. Please. I mean they're sitting for my for my My nephew. I love the stuff and out of him When you send these angels down to Sodom and gamora or two towns Abraham's thinking in his mind In two towns there's got to be 10 decent people in two cities There's got to be I'm my god everybody Can't be a pervert in both cities I started at 50 I knew that was high. Abraham said he's like he's playing blackjack He works jahovah down He works him down intercessory prayer works jahovah down He got him down to 10 And he stops at 10 Eric he stopped at 10 See Looking back on the story. He should have gone down to two But he's he's saying to himself in his mind I've just prayed through there's got to be for god's sakes five decent people in Sodom Jesus there's got to be five decent people in gamora I mean there's got to be He stops Angel show up.    Why you're going to be above The torch Right The torch is going to go out 75 80 square miles Sodom gamora zohar all these cities around here are loaded with perverts They're all going to burn it's over If you're in the mountain looking down You'll be saved Okay lot goes Hold on a minute I live in a democracy I don't want to go up in the mountain I don't like it there Zohar is over here a few miles away I'll go there Zohar is also full of perverts So he takes his family To zohar why they're running out of time The angel says okay go to zohar then but get out of here You remember the story don't you? No All right, let's read it then I can't do anything until you're out of here Why? Abraham already interceded for Abraham Didn't sit around questioning God's ability to help now. Let me think about this for a second here. My goodness Can he save lot?  Is he able to save lot? How would he do it? What kind of miracles would he take to save lot? How does he wanted to Abraham didn't give one thought to anything Except asking God to save Snafu period Didn't need any more details why? Abraham didn't live in a democracy. He lived in a monarchy. All he had to do was have a yes From the king of the monarchy. It was color. There wasn't any need to analyze it any further There's no need to get any more information. I don't need any information to pray All I got to do is lord per adventure you find 20 there Would you do and he said no, I'll save the place for 20. Well, let me ask again then Great lord, would you find 10 there? Would you let it go? I'll find 10. Yeah, how about How are you going to save her? You're going to put a special holy ghost bubble over him? I He didn't ask one question. He didn't care Abraham lived in a monarchy all he had to have was one word and it was done Zoar means small What happened? That city zoar lasted several hundred years god supernaturally saved it why Because you can get exceedingly and abundantly above All you can think and ask if you will obey god and not question What was she told to do? Lot and his wife had a kind of an American type of man marriage, you know, they're running the zoar Right and he's running ahead of her. She's back there. Are you not looking? No, he's scared. He's busy Well unbeknownst to him and the daughters mom's Trailing it She's hey, this is wait a minute for a second. Let's stop and talk about this Or is this really going to happen? I don't know burning the whole thing. Is that gone They told them not to look back See she lived in a democracy. She thought well, wait a minute. I got a vote here I can vote whether I look back or not See if you'll stop looking back when god told you just to go for Your miracles are all ahead of you. None of them are behind There she is to this day Yes, sir, she about used him And that's where she stands and jordan right there There it is right there see it all See all this salt there's zoar Somewhere down in the south of the red sea there with Sodom and Gomorrah Burnt the place up they've got sulfur all in that area to this day Zoar survived several hundred years there it is see it See him down there all this area here was the torched blaze The burn Thank god the lord doesn't handle Sexual perversion like that anymore Uh, I'd be lit up years ago Thank god for mercy and the blood of jesus in the cross of Christ Wow I would not trade places with that People in the old testament. No, I need mercy. How about you? Oh my goodness. There's moses.   This is symbolic for the The son of god when I send him Speak to that mountain There's the rock or speak to If you say into this mountain be thou removed be thou cast in the sea and do not doubt in your heart But believe that those things would just say come to pass it shall happen Just like you said it Moses speak to that mountain there in front of the congregation and the water Will come flowing out no problem Ambal Paraphrasing You shall give it to the congregation so they can drink and their beasts. That's the Hebrew word behemoth. It means Domestics, you know cattle sheep that kind of thing moses and erin gathered the congregation before the rock Moses is still mad Okay, listen to me now And I understand where you're at. I've been there. I've been mad at god in my past and I've gone through That myself. I know how you feel and exactly how you feel exactly You get mad at god and you're not going to be able to think straight You're going to say things and do things that you wouldn't do under normal circumstances see Yeah, I understand that you're married. Oh, yeah, they're driving you crazy. You got kids.  They're they're out of it Hey, we're griping about this.  He's got a twitch. He's got a torque in his neck Moses is gone stark raving crazy Am I criticizing him? No, I'd be right there with him Aaron's dragging a club foot now the Jews are driving nuts Listen, don't worry about it. I got it covered for you. Just speak to the rock calm yourself down Calm down Calm it down Bring it down Speak to the rock Moses heard it did everything right except one thing. What was that? He couldn't control His temper He had a temper problem Temper problem 42 years earlier.   Listen when you are angry or you're bitter against god or you're upset at someone you start to think it's you Providing these benefits You start losing your mind you start losing your focus you start losing where your source came from He says must we Provide all that hey, Moses dude calm yourself down This is the holy ghost split in the red sea you didn't do it remember you were on the shore yelling at him He yelled back at you. What are you talking to me for go?  I don't remember how that happened. I don't oh my god. I got those prayers answer I should have known that what was I doing? I should have stayed calm because I had gotten another prayer answer Just like I did this time in that time in that time two and three and two six year But when you get mad suddenly The stories go off as empty You want to get some water out of the rock?   Oh Both of Lost the promised land you will lose your promised land which we call your destiny If you don't stop voting And start obeying like that Jehovah calls moses aside.   Don't you? Who are you sucker? They didn't know was him They didn't recognize him as their deliverer That same story were used by god to the jews when jesus came They never recognized their deliverer again. They missed moses. Then they missed the load He left Egypt You know what he did for 40 years moses had a like a genius IQ This guy was a high octane performer. He wasn't a No offense. He wasn't guy loaded trucks This guy ran the corporation. He was the ceo not the janitor. No offense to janitor janitor is fine Mom's telling you what moses was this guy was 150 up here or something yeah You see you can be a very intelligent person And if you've got a bad temper you've got a bad attitude God may take a very accomplished person And reposition them in a new career. You know what that is sniffing sheep's butts Yeah, you may end up Sniffing sheep for a living and you might end up doing it for 40 years in the desert Why did it take 40 years?  Everybody's missed the whole bible study Akin oh, no not this guy. No, buddy, please joshua chapter six Jehovah tells joshua the same thing he told He told uh salt. Oh, man. Listen When these walls go down go in there and wipe this town out Okay, but don't bring back any of these things. They're either dedicated to idols.   It's all cursed Go to your house tonight and pick out everything that's demonic Find a trash can quickly tomorrow morning throw it out Well, I had some new age books when I was in college.  Do you need do you need another tick or something?     You flat broke you obey you get a miracle The only people saved in that whole town everybody died Except lot in his two daughters Rahab the whore and her family That was it why They obeyed when they didn't understand You do what you're told and your life will change fast friend. Don't bring any, uh Haram in my house Don't do that It'll bring a curse on you When you take the curse things make sure They're not in the camp because it will cause trouble That's what you did.  You bought a brought a cursed person into your home You started dating somebody with demons We had no idea what their background was. They had curses in their family tree. You got involved with them Now you got trouble We can remove that trouble tonight Guess what happened Aiken Oh that poor guy He saw He saw some goods What happened? I'll tell you what Greed is one of the most powerful Emotions of the soul you'll ever see Greed is incredible Just today I was talking about somebody whose family is Fighting like cats and dogs over their parents inheritance and they're not even dead yet Parents are old When you get old People start looking at you different. I'm not that old yet They're fighting because They live in anaheim california and They'll Two three houses a couple of small apartment complexes. They've got And some assets out there Okay, that's not That's not like massive here out in southern california. That's a worth a lot of money, right? There's three daughters This daughter here has five kids This one has none. This one has two The one that has none and the one that has two they're low-key about it Get around greedy, but the third one that has five kids Wants a bigger cut of a pie because She has more children Right So now they're fighting over it and it's causing hard feelings among the group Greed is a horrible disease that rots out the soul. This poor guy Took that Curse thing why he took a wedge of gold, right? That has Sean is it it means tongue in a ox And it's like what we have wedge of gold Looks like a tongue cow's tongue That's what it means 50 shekels silver See that wedge we have that's a wedge we would have There's looks different those are shekels they had Some famous person on one sign and then some symbol for a god on the back side They were made out of pure silver. You see them I took them at home and I did what I hit them in my tent Now listen the bible says that In Deuteronomy, Jehovah said listen If that if the dad sins You don't kill the kids If the kids sin, you don't kill the parents Right Deuteronomy That's what he said What happened to with aching? Well something bad happened here. The whole family was stoned to death So they must have all been in on it And he brought that stuff back that beautiful robe The wedge of gold the Bucket of silver coins wealth. They're wealthy now. They're rich When they get to the promised land he's thinking ahead They're going to be Upper crust when they get home Right So he buries it and hides it What do you do? Aiken's name stands for what in Hebrew it's a con It means Trouble yeah some reviewer trouble tonight What do you do less of the ice he saw the goods right Loss of the flesh he coveted them the pride of life. I can get away with us. I'll take it And then what do you do what everybody else does? You have to hide your sin You keep it hidden And that hidden sin Locks your blessings in your miracles from God Because you were told to get rid of it See if you hide iniquity in your heart the Lord will not hear you. What is iniquity? It's the evil in the heart that generates sin in the behavior Lust in the heart generates sinful sensual behavior Greed in the heart generates stealing of the body It's a sin to steal But it came from iniquity in the soul He saw it He lusted after it He took it and then he had to hide it The problem is friend In the spirit world Yet nothing is hit If you sin or you cheat or you lie or you say something when you're alone That was picked up in the spirit world. The holy ghost heard you the demons heard you Now they know what you think now. They know how you feel they will then plot against you To ruin you with the information you voluntarily gave them The holy ghost saw Aiken take that cursed greed Robe See in the new testament you are to be clothed with the righteousness of God Aiken took a Babylonian demonic robe Clothed himself with it and it cost him his life And his whole family was in on it Daddy, what do you got? Oh, I got all this look. Okay. Listen. I'm going to bury this stuff in the tent.  I had nothing to do with it.    God told you not to do it Well, my friends were doing it I asked some other people about it. I saw them doing it. I live in a democracy I just did it. I'll just do it You were told not to lust after people and chase after them for their sex and stare at their bodies and lust after them And masturbate over them. You were told not to do that by God You care do it anyway. Hey What do you expect me to do? Not married. I don't have there. You got a lot Rack of excuses there. You just went and did it When you do your alms. Hey do it in private. No, hey, I can't do everything in private I got to get some appreciation.  God will take care of the holy ghost got you covered It don't matter if anybody sees you or says hi to you or likes you or thanks you He sees you. He likes you. He's taken care of Well, you said no, I don't I'm Screw that.  Well, I don't have a good job.  I'll just do what I want because I live in a democracy. I like fine things. I like money I like a career. What about this? What about that? I need a better car. I need a better life.   The holy ghost wants to heal you. Stop it.  You're smart. Yeah Yeah, you're like freido on the godfather. Hey, I got stepped over mic. I'm smart Yeah, you're smart. You know where else you're smart and smart enough. Can you swim? Can you swim freido? Can't swim, huh? You can sink to the bottom That's what you're going to do You're going to sink to the bottom If you don't start obeying Without debating you look back on your christian life tonight You'll see it God told you to do that this and that and that and you didn't do it You had an excuse You didn't agree You couldn't do it. You didn't have the time you didn't have the energy blah blah blah blah You never did it You're going to stop that You know why because you unlike 90% of other christians don't want to waste your life You do not want to die a spiritual also ran you don't want to do it You do want to find your destiny Well, that's never going to happen Until you start obeying Without debating and asking questions Hmm Oh ramifications of that can I have What am I going to do about it? What am I going to do? Who? What? Where? Where? How? You've got to stop that demonic insanity This is a monarchy not a democracy. That's where you live You've been called by God You've been called by God to obey If you obey you get it exceedingly and abundantly above Whatever you think or ask according to the power dunamis that's supernatural power that works in you Where does that power come from a positive attitude? You've got the holy ghost living in there He's all the power anybody needs and then some Putting it mildly You know what you're going to do We repent tonight. I don't know what I should repent of Well, then you must be deaf You're going to repent of living in a democracy You don't live in a democracy if you're in the kingdom of God You're in a monarchy that's ruled by a royal family. I'm not talking about those crackpot imbeciles in great britain They're certified losers. I'm talking about divinity The divine monarchy god the father god the son and god the holy ghost A divine monarchy They tell you I want it done this way and you don't ask They tell you to jump you ask how far do I jump?  I heard you you went. Hmm I heard you You're going to repent of this tonight Say The things that make you go.   I've been doing my own thing for years I've been trusting my own mind and my own thoughts for years I make all my own decisions. I'm going to repent of that tonight I'm going to let you Tell me what side of the boat to throw the net on And I'm not even going to question why Even if it makes no sense to me I am so sorry lord That I questioned what you said I apologize for that I'm so sorry I took matters into my own hands I should have never done that I'm so sorry. I tried to fix My kids my spouse myself my parents I used my own skill and knowledge My own words my own verbiage My own self to fix people I saw that were Broken and they needed to change and they were wrong and I did it myself And in the end Everything got worse I'm sorry lord I should have just done what I was told And I would have been healed Healthy and happy I do want to find my destiny tonight. I do want help God saved me. I must Move out of my democracy I must move into my heavenly father's monarchy I must do that I'm asking you tonight lord Forgive me for being my own boss Running my own life And doing what I think's best I am so sorry I do not have those skills To make those decisions about my life or anybody else's come out of there devil I don't have those skills to do it. I don't have it I'm gonna repent right now And I'm getting off My little throne.   I'm gonna surrender my will come out devil.     Come on.  The bible says that lucifer is the king of pride Elegance greed Come on ladies Ladies you gotta have it. You gotta have the clothes The makeup The looks the car the jewelry Repent of it Repent of it.    That's all you got.   Your spouse's demons transferred into you Because you wouldn't shut your mouth The king of pride comes out tonight In jesus, my name Father let this cup pass for me Nevertheless come on say it Say it The most powerful words In history Nevertheless Not my will Be done The holy ghost is here anybody can get healed Anybody can get delivered The holy ghost is here. He's moving now He's moving now Reach out and grab him reach out with your guts Don't pray. It's simple little prayer. Stop that pray with your guts Pray with your guts come on Jesus God save me pray like that Come on Come on arrogance pride religious demons Religious demons just do it Just do it When the lord says thus say if the lord you just do it You don't ask You don't question. You don't think about it.  He saves those who have a contrite spirit You make it all the decisions. You're the boss.  You're in charge Folks we're in deep trouble now You're in deep trouble now If you will obey the lord of lords God will pour out his blessings on your life And you will not be able to contain it You are only one night of repentance away from a new life Turn from your sin now quickly Right now Come on Lay your excuses Down at the cross of Calvary My husband's crazy. My wife's nuts. No, that's an excuse. Lay them down here Lay them down. I don't have anybody to help me. I'm all alone. That's an excuse No, say for lord. I will never leave you no forsake me. You are never alone. That's an excuse. Lay that down You're never alone. Lay that excuse down Nobody loves me. Nobody cares me. That's a lie. That's an excuse That's an excuse. You're loved with everlasting love and with loving kindness.  Come on buddy right now. Quicker come out now All of them Every spirit Everyone out Come on now Come on now Come on now.  You don't understand.    He made it so you would pick up demons. He spreads demons through porn Why do you think there is porn?     Just do it Just do it Say to him come out now not tomorrow.    My name is Anthony and your name is Mike Mike, did you get one of my cards? Huh? Did you get one of my cards? No I haven't Yeah Hi Hey you mind giving him one of my cards?  You live here?  Okay Yeah I've had it when I was It's very horrible with names There's a couple of people I've had one on one I've spoken a lot with I'm Ron I've spoken a lot with Ron Give me a call and I'll pay for your bus fare when you get here okay I'll be happy to do it I'll sit down and talk to you okay Nice to meet you YouTubers Listen to me Put your hands on your head Get your demons to come out of your brain They got in through smoking pot Drugs Video games Video game demons get into your head Then they take over your mind Video games I curse you tonight I command you to come out Video games Get out of my head Get out of my head Just do it Just do it YouTubers go to the website hardcorechristini.com Hit the teaching button There's two articles you gotta read Hopefully one of them is how Satan controls the mind The second one, Satan's counterattack You will be hit Within 48 hours of this service 48 hours The devil's gonna hit you Satan's counterattack Next Friday 7 o'clock I'll be back


Most likely to get beaten up. How do you five? Who is the biggest simp? Why is that? Oh, I don't know. I just got all the girls. So it's not my fault. Who's the biggest mama's boy? What do you have to say? I love my mom very much. Who would be the one that's most likely to get beaten up?   I'm a lover. He's a lover. Who is the most trash at gaming? No, they're just jealous I beat them all. Who's the most afraid of their dad? And finally, who's the biggest teacher's pet? Do you get straight A's? Yeah. Who's your team? Rabbit A's. Ah, Dolphins. Nights. Up the walls! Dolphins. For the next five seconds, be as keenly as possible. Go. Turn my heel.


I'm Heather Gamsby, I'm the Spelling Communications Librarian here at Memorial University. Open access is very important both for researchers and writers. For researchers they can access anything around the world when it is openly available through open access. Yeah, probably our most popular thing is our open access fund where we help fund the article processing charges for any month author, it could be an undergraduate student, faculty member, staff member, because article processing charges can be several thousand dollars. The research repository has our electronic theses and dissertations. So all of the new theses and dissertations that are put up by the School of Graduate Studies come into the research repository. A lot of subscriptions to journals have increased over the years. It's the big deal where a lot of journals are bundled together, a lot of libraries are breaking away from that. So open access is just one side of the coin that there is the closed access aspect to it all to kind of account for. So these two things are kind of struggling against one another as time goes on.


Welcome back to the Riffamonus reproducible research tutorial series. I hope you're able to make it through the last tutorial in which we used Git to document the evolution of our data analysis. As I mentioned in that tutorial, we'll continue to use Git as we proceed with the development of our analysis. I think it's worth emphasizing that to get the most benefit from Git, you really need to regularly commit your changes. There's little point in resolving to use Git, but only committing at the end. That kind of misses the point. In today's tutorial, we're going to follow up with a question that I asked at the end of the last tutorial. If I were to accidentally nuke my project directory, how difficult would it be to get back to where I was before the disaster? I could use version control to get back all over code, but it might be a bit difficult to pull together all the pieces unless I'd already planned for such a calamity. Today we're going to be discussing how we can use bash scripts to automate our analyses. This will minimize our involvement in running individual steps. At the end, I'll intentionally delete my directory and show you how we can get back up to speed. Remember that our primary motivation is to be a better collaborator to our future selves. So if we can pull off the feet of nuking our directory and then regenerating the analysis, then we can be pretty confident that our analysis is close to being reproducible by ourselves as well as others. In today's tutorial, we'll make use of some of the mother scripts that are built into the new project template. You don't need to know how to use mother for this tutorial, but it's a great program that you should definitely be familiar with if you're doing any type of 16s rRNA gene sequence analysis. Now join me in opening the slides for today's tutorial, which you can find within the reproducible research tutorial series at the rifomonas.org website. Before we get going on today's tutorial and talking about automation, I want to remind you of what we talked about in the last tutorial in using version control. And so here's a little exercise that I'd like you to think about with me for a couple of moments. So let's assume we've made a few changes to our readme.md file to update the versions of the software packages that we're using in our analysis. What are the commands that you would enter to commit and push those changes? So go ahead and hit pause and think about what those commands would be and perhaps even write them out. So how difficult was this for you to remember? Again, by repeated practice of writing these commands in actual projects that you're working on, it'll become something like second nature. And so here's what I would recommend doing. So again, we start with git status as the goal being to see what files have changed. Git add readme to add it to the repository to add those changes. Another git status to make sure that we're getting ready to commit exactly what we want to commit. And then we're going to write git commit-m with the message update versions of software packages. Again, we want a pithy declarative imperative statement about what has happened.  And then we can do a git push. You should also note that if you want to be super careful, you might also want to run git pull before the first git status. This will make sure that you don't have any conflicts if perhaps you changed something on the GitHub website before you'd made the changes to your readme file. I always forget that I make these types of changes and so it's a good practice to put that git pull in first. It doesn't really cost you anything and it saves you problems down the road. So for today's tutorial, we have several learning goals. The first is to appreciate the value of automating your analyses. I've already talked about that a bit in the introduction earlier. We're going to build executable scripts that contain analysis pipelines. We're going to differentiate between absolute and relative paths and which one you should be using. And then finally, we're going to identify the limitations of having a driver script like this, which we'll point forward to a few tutorials from now when we talk about other approaches that we can use for automating this type of work. So hopefully you'll remember the noble manuscript that we read a few tutorials back. And in there, he talked about a driver script. And we kind of put that to the side at the moment while we were talking about project organization. Some of the points that he made, as you might remember, would be to record every operation that you perform, comment generously, don't edit intermediate files by hand, use a driver script to centralize all processing and analysis, use relative paths, and make the script restartable. All of these elements relate to what we're going to talk about today of having a driver script. So when we think about recording every operation that we perform, it's important to keep in mind that any analysis you're likely to perform once, you'll probably actually perform twice or three times or four times or five times. And so by having these steps recorded and perhaps made to be automated, it'll make it that much easier in the future. Your mental model as we do this should be that someone is going to download your repository and try to rerun your analysis. So something to think about would be someone, perhaps you, a nuke the contents of your data directories. How would they regenerate figure one? What steps would they have to take to go from nothing back up to being able to generate figure one? Keep in mind that's likely to be you more than it's likely to be someone else. Alternatively, if you were to go home for the night, can you keep the analysis working without having to be at the computer? It's really nice if the analysis is automated so that you can fire up your AWS instance, use Tmux, start your driver script, and walk away and come back in the morning and hopefully your analysis has been completed without you having to do anything more. So if this isn't possible because say you're using a GUI, like I talked about earlier using the ARB software, you really have to take explicit notes that are available for others, and again including yourself. Comment generously. In Bash and many other scripting languages, you can use comments where you put a pound sign before the comment. That pound sign will tell Bash or R or whatever language to ignore everything that follows. We all are code readable and self-documenting as much as possible. And at a minimum, each script or section of a script should have a header that indicates the inputs and outputs and what's going on in this script. Do not edit intermediate files by hand. Again, we want to keep our raw files raw. And so if we start from raw files or files that are downloaded, your script is going to provide the provenance of each derivative data file. That by scripting it, we're automating that analysis and we're not going to write over earlier files. Going back to that paper airplane example, imagine how much more uniform, reproducible and fast the construction would be if it could be programmed. I just love these videos of automated paper airplane folding. Again, this is what we're going for as we think about our data analysis pipeline. We're not so interested in folding paper airplanes perhaps, but we are interested in folding our data analysis, right? We're interested in starting with a blank directory with some code in it, launching that code and coming back and finding that the code's been run and we've got data directories that are full of raw data and process data and eventually perhaps a written manuscript. And so we'll get there eventually. Use relative paths. This first example is what's called an absolute path. And so you know it's an absolute path because it starts with a forward slash. This forward slash at the beginning indicates the root directory. And so this entire path tells the computer how to get to the readme.md file that's in my data raw directory of my project relative to the root. And so if it's relative to the root, that's what we call an absolute path. The second example is what we call a relative path. And so assuming that we're in the root of my directory for my project, say Kozitch re-analysis Sumbio 2013, this tells the computer where the readme.md file is that I'm interested in. It's relative to the root of my project directory. This readme.md then is a file and we'll assume that it's within data raw. So why are we interested in relative paths, which I would say is the second example. Well, if I were to clone this repository to my local laptop, I will not have a home directory called Ubuntu. I have a home slash pshloss, but not home slash ubuntu. And so my computer will throw an error when it tries to find this readme file using this absolute path. However, if I clone the repository and then cd into the directory of Kozitch re-analysis Sumbio 2013, and then I say data raw readme.md, my computer will find that because it's relative to the root of my project directory. However, if I say readme from the root of my project directory, it's going to give me the readme for the overall project, not the one in data raw. You could assume that somebody's going to cd into data raw, or you might provide code to cd into data raw, but that's dangerous because if there's an error at some point and that cd command doesn't get run, then it's going to again be looking at the readme in your project directory. So it's always best to run your commands and assume your files are in a location relative to the root of your project, not relative to the root of your computer, or that the user or you are moving around using cd commands within your project directory structure. So use relative paths. Make the script restartable. So we'll save this for later when we learn about make, but the idea is that if we only change the script to plot the ordination data, we shouldn't have to also then re-download all the raw data. That the automation is smart and it knows where we are and it can keep track of the dependencies. Unfortunately, the reality is that most bioinformatics tools, things like Mother, Chime, Velvet, are run from the command line and they're not meant to be interactive. By interactive, I mean things like Microsoft Excel or Arb, where you're going in and you're manipulating data and you're adding code, you're selecting different sequences, and they're not really meant to be interactive on that scale. They're meant to take in commands, the program then runs the command and it spits out output. The other reality is that you probably also don't want to run big analyses on your laptop. You need to run them on a computer cluster, which is why we're using the Amazon EC2 service. Also, few computer clusters will let you run your programs interactively. You'll end up submitting jobs, as they're called, which then requires special scripts. Again, to think of that motivation I mentioned earlier, where you want to fire up your analysis, say at five o'clock on a Friday afternoon and come back on a Monday morning and find that your analysis is completed. To do that, we're going to be needing to use special scripts to run our analysis, these driver scripts, as Noble called them. Bash scripts can be very straightforward or very complicated. We want to keep them fairly straightforward. It's a script file as a text file that contains commands that you would otherwise run from the command prompt. It's nothing magical. It's a text file that you could copy in all of your commands to then tell as instructions to the computer for what it needs to run. We're going to return now to the Cosetree analysis and add the download scripts to a new driver script to start building up our driver script. As we do this, we're going to be sure to add comments. Of course, we're also going to be using the Amazon EC2 instances that we've been working with on previous steps of this project. I'm going to log into my instance here. This should hopefully be becoming second nature to you. I will open up my terminal, copy the IP address here, and I'll go into my Cosetree analysis directory. If I ls that, the instructions for downloading my raw data are in my data-raw-readme file. I can do nano-data-raw-readme. The lines that I'm interested in are this wget-tar-rm. I'm going to go ahead and highlight and copy these lines. I'll do copy and I'll quit out. Now I'll do nano-analysis-driver.bash. This opens up a new directory. I'm sorry, it opens up a new file and I'll do paste. This is markdown, and I'd like to convert this into comments for my new analysis-driver-bash file. I'm going to put a pound sign ahead of these lines. I can get rid of that and that. Just to make it look a little bit nicer, I'll put some spaces in there. I've called it analysis-drive-bash. I'll rename it analysis-drive-to-analysis-driver.bash. Let's go ahead and also get the reference files for the Silva and the RDP training sets. Those are stored in my data-references-readme file. Again, I can highlight these lines. Copy and nano-analysis-driver.bash. Then I'll come down here and I'll fix my commenting. Comment there. To get rid of this entire line in nano, you can do CTRL-L. I'm sorry, CTRL-K. CTRL-K. It looks like some weird stuff happened here. This should be taxon bacteria in the mother code. Down here, then, I can put a pound sign there. Again, CTRL-K to get rid of that bash and get rid of those three backticks. Again, what I've done is I've copied the text from my readme files into this file-analysis-driver.bash. All of the instructions are here. There is code now for these. Again, if you're using the exact code I am, it should look like this. You might have the code that you used when you created your readme files in the previous tutorial. I'm going to go ahead and save this and exit out. One other subtle thing that we need to add to our bash script here is at the top, a line called the shebang, the whole shebang. That is pound exclamation point, forward slash user, forward slash bin, env space bash. When we run this file, this will then tell the Linux system what to be running, and that we're running bash to get this. We can save that. See, we get some special coloring because we tell it it's in bash and we exit out. Now I can run this as bash-analysis-driver.bash. If I run that, you'll see that it downloads and runs everything. I'm going to speed this up a bit because it looks like it's going to take it a little while. It finally finished. It took a few minutes to run through and download and move things around to where I wanted them. I can type ls, make sure that everything looks clear there. If I do ls data raw, I see that I've got my raw files here. Everything looks on the up and up. If I do ls data forward slash references, again, I see my files here as well. It looks like everything is where it's supposed to be. Now what do we do? If you said we need to commit, you're right. Let's go ahead and do get status, get add analysis driver bash, get status, get commit dash m, and I will say add code to obtain raw and reference data. Get status. We're good to go. It looks like previously I forgot to push this. We'll save a push later, but you might want to push at the end of every day that you're working on your project or every couple hours, again, just as a backup for what you're working on. The next thing we want to do is we want to start analyzing this data using mother. You may have noticed this already, but if you look at ls code, you'll see a number of batch files in there for running mother commands. If we do nano code forward slash get good seeks dot batch, you'll see some mother commands in here. Let me make my window a little bit bigger. You'll see that some of the commands take up multiple lines, but these are all mother commands that we can run by doing mother code get good seeks dot batch. I'm not going to run this right now, but this would be how we could run it for mother. I'm going to hit Ctrl C to get off of that line, because I'm going to put this into my analysis driver batch file. Let's get good seeks batch file again. Just to point out a couple of things, if you're using this for your own data, one thing that you would want to change in here would be that we have in make dot file the prefix stability. The data relates to a stability analysis of murine gut microbiota. Say you're doing something related to soil, you might really change this to soil or antibiotic treatment, you might change this to antibiotics, whatever you want to give a prefix to the files that will be generated by mother. Another thing that we should note when we look at this is that we are using relative paths. The input directory is data raw, the output directory is data mother. We're using relative paths throughout here. One other thing that we want to double check is that we have all the files. We've seen that our data raw files are there. One file we might want to check is to make sure the Silva v4 aligned file is there. We also want to make sure that our data references train set file is there, as well as the pdsFASTA and taxonomy files for that. Let's Ctrl X out of that and do LS data references. We see the train set files here, the FASTA and the tax, but we don't see a Silva v4 file. To do that, to generate that file, we need to run some other code. Let's go ahead and we will do nano driver analysis driver.bash. I'm going to come down to the bottom of that file and I'll create a comment that says generate a customized version of the Silva v4 reference data set. To do that, we'll do code forward slash mother forward slash mother space pcr.seqs I need a pound sign. This is a command line version of running mother where you don't have to go into mother, but you can run commands from the command line with mother. We'll do fast dot equals data reference forward slash Silva dot seed dot align start equals 11894 and equals 25319 we'll do keep dots equals false and processors equals 8 and then we'll close that with closing parentheses and quote and we'll also then do MV data forward slash references references which reminds me getting scatterbrained here that I have a reference here data references so fix that data references Silva dot seed dot pcr dot align and we're going to move that to data references forward slash Silva dot v4 dot align and so again this is some inside baseball if you will about running mother but we can generate a version of Silva seed align which is in our data references directory that targets the v4 region and so if we save that and exit out just want to briefly show you if you come generate a new tab and we go to mother dot org wiki main page that there's a link here for the my seek SOP and what we're following in this code is all embedded in this wiki page and so somewhere in here further down right here we have the pcr seeks command that we just put into mother as well as renaming the file so we could have used rename file but we did that with an MV and so that should work pretty well and so if you're wondering where all the commands come from in those batch files I've given you they're all listed here so we could do is we could again do bash analysis driver dot bash but that's going to download everything again and so this is one of the problems with our analysis driver bash file as we currently have it so I'm going to do control C and one of the things that we can do is again do nano analysis driver bash and I'm going to come down to the bottom of this file and I'm going to highlight these lines copy them quit out and then paste the lines into the command prompt and it will then run my mother code it's running the pcr seeks command and so it runs through aha and it says cannot stat which means it can't find data references silver seed pcr line knows such file directory you see what I did wrong I misspelled references so let's go back into nano analysis driver bash and let's fix the spelling of references save that again copy and paste these lines paste them back in and hopefully we run this and we don't get any error messages so that works great again if we do ls data references we see that we have the silver v4 aligned file okay great so what do we want to do let's commit it so to get add analysis driver bash get status get commit dash m add code or we'll just say generate silver dot v4 dot align file right great now we want to add in some more of those mother commands so the nano analysis driver bash come to the end of the file and we want to run mother through the data curation steps and so to run that we'll do code forward slash mother forward slash mother make sure we spell it right and then code get good seek dot batch and so we'll go ahead and save this and just to prove to you you'll notice in this nano file that we're running code mother mother that the path to mother is in code in the mother directory within code and so if we do ls code we see there's a directory for mother ls code mother we see that there's various executables and so if we do code mother forward slash mother we see that we open up mother and so again this proves to ourselves that mother is where we think it is we can type quit ls and we can get back to where we were so again if we go back to that analysis driver file we can highlight this line of code copy it and then run it in our terminal window and so again what I did was I pasted that line in and now mother is going to run this and it's going to take a bit of time and so I'll try to speed up the output here so great the analysis finally finished as I said I sped it up here what you might notice is that I lived on the edge here and did not use Tmux to run the analysis so running Tmux probably would have been a bit safer because if for some reason my internet would have gone down the analysis would have kept running even though I would have been logged out of EC2 alright so the next thing we'd like to do is to run the next batch in our analysis workflow so if we do ls code we can see that the next is in the pipeline is git error batch so I'll do nano code git error dot batch and looking here at what happens this uses the mock community data in here to run the command seek dot error but one reference file it needs is HMP mock v4 fast day so let's double check that we have that in our reference file so if we do ls data references I do in fact have an HMP mock v4 dot fast day file so we should be good for that so let's go to our analysis driver dot bash file and again scroll down to the bottom and run mock community data through seek dot error to git sequencing error rate okay great so we'll do code mother forward slash mother code git seek error I'm sorry git error dot batch again we don't want to run the whole script right now because it's going to take forever we'll come back and we'll do that at the very end so we'll copy this and paste it in so the next step in our mother pipeline is to run git shared otus dot batch so let's open that up and see what it looks like and so we see that we're going to remove our mock community samples we'll run it through clustering we'll then make a shared file and we'll run classify otus so the other thing to keep in mind is that if you way back when we ran make dot contigs we used the prefix of stability so if you change stability there you're going to have to change it in all of these batch files but that's the only place you would change it is in the first command from stability to something else so we'll get out of that and do nano analysis driver batch and we'll say something like run process data through clustering and making a shared file code mother mother code git shared otus dot batch and again we'll copy that and we'll do paste it so now we've run everything through mother and we've gotten our shared file which if you're familiar with mother you'll know that shared file is the file that we use for all the downstream analysis of looking at things like alpha and beta diversity we also have our error rate data so a couple of things that we still need to do include generating an ordination for that figure that we want to be able to put into for that figure that associated with the paragraph that we pulled out of the manuscript and we also need to rarify the data to get the number of otus that we are seeing in our samples let's go ahead and commit what we've done so far and do git status where we've modified our analysis driver dot bash file so we'll do git add analysis bash git status git commit dash m load pre-baked mother batch scripts to driver script status alright so we're all up to date so the next thing we'd like to do is to build an ordination diagram and to do that we're going to be using our shared file and the mother file names as you may know can get pretty long and so let's go ahead and find that file so if we do ls data forward slash mother and it ends in shared so we'll do star shared and we see this long file name so if we copy this it'll make it a lot easier to enter the command so let's make a new file so we'll do nano code forward slash git nmds data dot batch and so what we're going to do in this script is we're going to run the mother commands to generate the file that has the nmds data that will eventually plot using r in the next tutorial so we'll do set dot current input dir equals data forward slash mother output dir equals data forward slash mother and we'll do set we'll do seed equals nineteen seventy six zero six twenty and then we'll do dist dot shared and we'll then add our shared file name so shared equals and I'm going to paste it in that and then we will say calc equals theta yc sub sample equals a thousand I'm sorry three thousand and I'll do itters equals a hundred and processors equals four so if you don't know what this all means don't worry about it this isn't a tutorial to teach you mother but showing you rather how you can use mother commands within a batch script and so if you're interested in learning more about this go back to that my seek SOP page and a lot of this will make sense after you look at that finally we can do nmds filip equals current max dim equals two so we'll save this and quit out and let's go ahead and test it by doing code forward slash mother forward slash mother code forward slash get nmds so if we run this what ran through generating the distance matrix for theta yc beta diversity calculator and then use that to generate nmds data and we'll play with that nmds data in a subsequent tutorial when we go ahead and plot that using r so we need to add that to our analysis driver file and so I'm gonna up arrow to get the previous command and I'll highlight that I'll hit ctrl c to get off that line I'll do nano analysis driver bash and I'll come down to the bottom to then say generate data to plot nmds ordination so we need to commit this change to get status and so we want to do get add code get nmds batch we also want to add the analysis driver dot bash file get status both of those have been staged we can now do get commit generate nmds ordination data excellent so again I need to get the long shared file name so if I can do ls data mother star shared I get this long beast of a name that I'm going to highlight and copy and then I will do nano get sobs data dot batch nmds sobs is our shorthand for the number of observed species or otus or taxa and again we'll do set dot current input dir equals data forward slash mother output dir equals data forward slash mother seed equals 1976 0620 and then we'll do summary dot single shared equals that beast we'll do calc equals nseqs sobs so this will tell us the number of sequences that it was rarefied to and the number of observed otus and then we'll say subsample of 3000 again and this will rarefied the data to get us 3000 sequences per sample we can save that and then we can do mother I'm sorry code forward slash mother forward slash mother code get sobs data dot batch excellent so that ran also so we're going to now copy this code that we ran into our driver file and we can go ahead and commit that as well great so let's go ahead and look at the history of our commits and we can do get log and we will see that we are keeping pretty good track of where we are in our data analysis pipeline and so if we wanted to go back to any point in our code history we could perhaps roll back a repository to a previous commit but we're pretty happy with where we are and this is looking really good so to get out of this view of the log you can type q and this brings us back to the command prompt so we've been doing a lot of copying and pasting into and out of our analysis driver batch file what we'd like to do is to make sure it all works but I'm going to up the game a little bit more I'm going to delete my directory and see if it all works there's one thing before we do that so I'll do get status and it says that my branch is ahead of origin master which is the github version by nine commits so use get push to publish your local commits so I'm going to go ahead and push it so I'll do get push enter my credentials okay there we go and so then if we come over to our github page I'm going to find my cosetree analysis repository just make sure everything's been updated and sure enough my analysis driver batch file is here if I click on that I see all my code here which looks great and I'm going to go back to my directory here and just give it one last look I'm nervous about doing this I'll do cd tilde ls I'm going to do rm-rf cosetree 3, 2, 1 delete ls oh no it's gone what do I do hopefully you remember from last time there's a command in get called clone we can do get clone and I can come back to my repository here and I can click on this green button copy the link paste that in and then I can do cd cosetree ls and I see everything's there but if I do ls data forward slash raw nothing's there right so we need to regenerate all the data all the analysis so I'm going to go to lunch so I'm going to run this in tmux so we can do tmux we're here and then we can do bash analysis driver.bash hit enter and away it goes so remember we can get out of this by doing ctrl B D and we're back here and I can exit out and and here we go now we're so and see where things are note that for now we do not want to stop this from running because it's running so while the script was running I realized that we never added instructions to the analysis driver script for how to get a copy of mother so what I did was to go into nano mother I'm sorry nano code and copy and then open up the analysis driver batch and paste it into the top of the file here so because we were getting error messages that it couldn't find a copy of mother we now have to rerun everything again so this is exactly why we do these types of scripts because we want it to be reproducible if you were to download this and it didn't have the mother code installed in a world of hurt it's great that we rerun it it's great that we saw that we were assuming some dependency was present being mother and it wasn't so we need to now go ahead and run it again I've already committed it let's go ahead and run batch analysis driver dot bash run it and we'll come back in another hour alright so let's try that again so we'll do tmux a and we see that it's getting to the end I think it's in the rare fraction step so we'll just sit with it here for a minute looks like everything's working well and voila it is done great isn't it awesome that we can automate our analysis this is looking pretty darn close to my April Fool's joke of a mother command called write dot paper you might think it's funny but in two more tutorials we'll actually write something that looks a lot like write dot paper look at the project that you're currently working on in your lab how automated is the analysis do you have a single file that describes the workflow even if it isn't full of bash commands it would be great to have a document that lists the steps and the commands that one would need to follow to go from raw to process data one thing you might notice about this approach is that it doesn't leave a lot of room for tools with a graphical user interface like Microsoft Excel those tools are fine and I don't mean to cast shade at them but hopefully you can see by now their limitation for doing a reproducible analysis it's really hard to document all of those mouse motions and the toggles that need to be said to repeat an analysis in that environment in the next tutorial we'll see how we can use scripting languages like R to further automate our analysis


Her done a great job in terms of really getting the sort of emotional touch and the human touch of the event, which was terrified the whole world. To that extent that the journalist herself gone into sort of understanding how they're going to cope up with this event and I think especially the emotional part of it, which I thought other shortlisted entries probably didn't had opportunity because they were talking about business. The other had an opportunity but didn't cover that way. So I think the winner definitely stands out quite nicely in this whole category.