Natya Hans

Natya Hans

Evolutionary computational biologist

Posts by Tags

DualAuthentication

Using HiPerGator without Dual Factor Authentication every time

2 minute read

Published:

Hipergator recently updated to a dual factor authentication for logging in, which means for people who use it daily and and need to login multiple sessions, it can get annoying pretty fast. The workaround is to use ssh multiplexing which can allow you to use an existing TCP connection for multiple sessions. More on multiplexing here. In other words, given that you log in and authenticate once, and as long as the initial terminal remains open, you can log into multiple sessions without authentication. Although I would advise against it, but you can increase the time from 8hrs.

R

Publication Quality Figures in R

1 minute read

Published:

This tutorial is written to guide relatively new R students on how to make a publication ready figures in R. It can be daunting to figure this out on your own and look at several websites to figure out which R packages are needed,along with how to fulfill each journal’s requirement for fiures, so I am going to try to keep this short and simple. Here are a list of packages that are needed and can be easily installed from CRAN.

RAxML

RMarkdown

Publication Quality Figures in R

1 minute read

Published:

This tutorial is written to guide relatively new R students on how to make a publication ready figures in R. It can be daunting to figure this out on your own and look at several websites to figure out which R packages are needed,along with how to fulfill each journal’s requirement for fiures, so I am going to try to keep this short and simple. Here are a list of packages that are needed and can be easily installed from CRAN.

RNotebook

Publication Quality Figures in R

1 minute read

Published:

This tutorial is written to guide relatively new R students on how to make a publication ready figures in R. It can be daunting to figure this out on your own and look at several websites to figure out which R packages are needed,along with how to fulfill each journal’s requirement for fiures, so I am going to try to keep this short and simple. Here are a list of packages that are needed and can be easily installed from CRAN.

RStudio

Publication Quality Figures in R

1 minute read

Published:

This tutorial is written to guide relatively new R students on how to make a publication ready figures in R. It can be daunting to figure this out on your own and look at several websites to figure out which R packages are needed,along with how to fulfill each journal’s requirement for fiures, so I am going to try to keep this short and simple. Here are a list of packages that are needed and can be easily installed from CRAN.

aliases

‘Setting up Aliases’

5 minute read

Published:

Setting up Aliases in linux and unix makes life a lot easier. You can choose your own commands and shortcuts to commands you commonly use a lot and save time. Another way to make life easier is to set up SSH keys so you won’t be asked for a password everytime you login to the server. Felicia did an excellent blog on it already, which you can check out here

allocation

Using dev version on hipergator

2 minute read

Published:

Allocating resources on dev

Hipergator allows the users to allocate resources for running simple applications on the cluster. Please see the criteria for short testing jobs allowed on Hipergator here. Remember that the developmental version is only for testing purposes, so do not submit any job that takes a long time to run. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

astral

bash

Using HiPerGator without Dual Factor Authentication every time

2 minute read

Published:

Hipergator recently updated to a dual factor authentication for logging in, which means for people who use it daily and and need to login multiple sessions, it can get annoying pretty fast. The workaround is to use ssh multiplexing which can allow you to use an existing TCP connection for multiple sessions. More on multiplexing here. In other words, given that you log in and authenticate once, and as long as the initial terminal remains open, you can log into multiple sessions without authentication. Although I would advise against it, but you can increase the time from 8hrs.

‘Setting up Aliases’

5 minute read

Published:

Setting up Aliases in linux and unix makes life a lot easier. You can choose your own commands and shortcuts to commands you commonly use a lot and save time. Another way to make life easier is to set up SSH keys so you won’t be asked for a password everytime you login to the server. Felicia did an excellent blog on it already, which you can check out here

‘Running jobs on HiPerGator’

2 minute read

Published:

Breakdown of Slurm Script

HiPerGator moved from a PBS to Slurm(Simple Linux Utility for Resource Management), in 2015? or 2016?, not sure.
But let’s break down the sample bash script line by line , which you can download here

‘Modules on HiPerGator’

less than 1 minute read

Published:

Modules on HiPerGator

The tutorial available on UFRC website does a pretty good job explaining how to load a software for running jobs on the cluster.
Click here for Module Tutorial by UFRC After you have loaded the list of modules you want to load, you can save the modules to a default list by,

Transferring files to the cluster (HiPerGator)

2 minute read

Published:

Now that you are on the cluster, let us learn some basic commands to navigate your way.First you need to know your location on the cluster. Type:

Using the cluster (HiPerGator)

1 minute read

Published:

If this is your first time using the cluster, I would advice to learn some basic bash scripting. Navigating your way through different directories and cluster would be a lot easier with basic bash commands such as pwd,cd, mkdir, ls ( Note to self: Make a post about it)

bloomberg

dev version

Using dev version on hipergator

2 minute read

Published:

Allocating resources on dev

Hipergator allows the users to allocate resources for running simple applications on the cluster. Please see the criteria for short testing jobs allowed on Hipergator here. Remember that the developmental version is only for testing purposes, so do not submit any job that takes a long time to run. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

digital

Digital Planner 2022

less than 1 minute read

Published:

Last year I created a digital planner using Keynote, since I wanted to use my iphone for keeping track of things. “Note” as a note keeping app is great but not I was looking for more organization in my schedule and reducing the clutter from my mind. I live in organized chaos so I wanted to give my mind a break.

disk usage error

free

Digital Planner 2022

less than 1 minute read

Published:

Last year I created a digital planner using Keynote, since I wanted to use my iphone for keeping track of things. “Note” as a note keeping app is great but not I was looking for more organization in my schedule and reducing the clutter from my mind. I live in organized chaos so I wanted to give my mind a break.

gene tree

‘Bayesian inference using MrBayes on HiPerGator’

3 minute read

Published:

Update on hipergator and allocating resources on dev

Hipergator moved it’s storage from ufrc to blue so the path should be changed to /blue/GROUPNAME/NAME/. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

hipergator

Using dev version on hipergator

2 minute read

Published:

Allocating resources on dev

Hipergator allows the users to allocate resources for running simple applications on the cluster. Please see the criteria for short testing jobs allowed on Hipergator here. Remember that the developmental version is only for testing purposes, so do not submit any job that takes a long time to run. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

Using HiPerGator without Dual Factor Authentication every time

2 minute read

Published:

Hipergator recently updated to a dual factor authentication for logging in, which means for people who use it daily and and need to login multiple sessions, it can get annoying pretty fast. The workaround is to use ssh multiplexing which can allow you to use an existing TCP connection for multiple sessions. More on multiplexing here. In other words, given that you log in and authenticate once, and as long as the initial terminal remains open, you can log into multiple sessions without authentication. Although I would advise against it, but you can increase the time from 8hrs.

‘Bayesian inference using MrBayes on HiPerGator’

3 minute read

Published:

Update on hipergator and allocating resources on dev

Hipergator moved it’s storage from ufrc to blue so the path should be changed to /blue/GROUPNAME/NAME/. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

‘Setting up Aliases’

5 minute read

Published:

Setting up Aliases in linux and unix makes life a lot easier. You can choose your own commands and shortcuts to commands you commonly use a lot and save time. Another way to make life easier is to set up SSH keys so you won’t be asked for a password everytime you login to the server. Felicia did an excellent blog on it already, which you can check out here

‘Running jobs on HiPerGator’

2 minute read

Published:

Breakdown of Slurm Script

HiPerGator moved from a PBS to Slurm(Simple Linux Utility for Resource Management), in 2015? or 2016?, not sure.
But let’s break down the sample bash script line by line , which you can download here

‘Modules on HiPerGator’

less than 1 minute read

Published:

Modules on HiPerGator

The tutorial available on UFRC website does a pretty good job explaining how to load a software for running jobs on the cluster.
Click here for Module Tutorial by UFRC After you have loaded the list of modules you want to load, you can save the modules to a default list by,

Transferring files to the cluster (HiPerGator)

2 minute read

Published:

Now that you are on the cluster, let us learn some basic commands to navigate your way.First you need to know your location on the cluster. Type:

Using the cluster (HiPerGator)

1 minute read

Published:

If this is your first time using the cluster, I would advice to learn some basic bash scripting. Navigating your way through different directories and cluster would be a lot easier with basic bash commands such as pwd,cd, mkdir, ls ( Note to self: Make a post about it)

inode

ipad

Digital Planner 2022

less than 1 minute read

Published:

Last year I created a digital planner using Keynote, since I wanted to use my iphone for keeping track of things. “Note” as a note keeping app is great but not I was looking for more organization in my schedule and reducing the clutter from my mind. I live in organized chaos so I wanted to give my mind a break.

iphone

Digital Planner 2022

less than 1 minute read

Published:

Last year I created a digital planner using Keynote, since I wanted to use my iphone for keeping track of things. “Note” as a note keeping app is great but not I was looking for more organization in my schedule and reducing the clutter from my mind. I live in organized chaos so I wanted to give my mind a break.

keynote

Digital Planner 2022

less than 1 minute read

Published:

Last year I created a digital planner using Keynote, since I wanted to use my iphone for keeping track of things. “Note” as a note keeping app is great but not I was looking for more organization in my schedule and reducing the clutter from my mind. I live in organized chaos so I wanted to give my mind a break.

linux

Using dev version on hipergator

2 minute read

Published:

Allocating resources on dev

Hipergator allows the users to allocate resources for running simple applications on the cluster. Please see the criteria for short testing jobs allowed on Hipergator here. Remember that the developmental version is only for testing purposes, so do not submit any job that takes a long time to run. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

Using HiPerGator without Dual Factor Authentication every time

2 minute read

Published:

Hipergator recently updated to a dual factor authentication for logging in, which means for people who use it daily and and need to login multiple sessions, it can get annoying pretty fast. The workaround is to use ssh multiplexing which can allow you to use an existing TCP connection for multiple sessions. More on multiplexing here. In other words, given that you log in and authenticate once, and as long as the initial terminal remains open, you can log into multiple sessions without authentication. Although I would advise against it, but you can increase the time from 8hrs.

‘Bayesian inference using MrBayes on HiPerGator’

3 minute read

Published:

Update on hipergator and allocating resources on dev

Hipergator moved it’s storage from ufrc to blue so the path should be changed to /blue/GROUPNAME/NAME/. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

‘Setting up Aliases’

5 minute read

Published:

Setting up Aliases in linux and unix makes life a lot easier. You can choose your own commands and shortcuts to commands you commonly use a lot and save time. Another way to make life easier is to set up SSH keys so you won’t be asked for a password everytime you login to the server. Felicia did an excellent blog on it already, which you can check out here

Transferring files to the cluster (HiPerGator)

2 minute read

Published:

Now that you are on the cluster, let us learn some basic commands to navigate your way.First you need to know your location on the cluster. Type:

Using the cluster (HiPerGator)

1 minute read

Published:

If this is your first time using the cluster, I would advice to learn some basic bash scripting. Navigating your way through different directories and cluster would be a lot easier with basic bash commands such as pwd,cd, mkdir, ls ( Note to self: Make a post about it)

modules

‘Modules on HiPerGator’

less than 1 minute read

Published:

Modules on HiPerGator

The tutorial available on UFRC website does a pretty good job explaining how to load a software for running jobs on the cluster.
Click here for Module Tutorial by UFRC After you have loaded the list of modules you want to load, you can save the modules to a default list by,

mrbayes

‘Bayesian inference using MrBayes on HiPerGator’

3 minute read

Published:

Update on hipergator and allocating resources on dev

Hipergator moved it’s storage from ufrc to blue so the path should be changed to /blue/GROUPNAME/NAME/. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

pagel

phylogenetics

‘Bayesian inference using MrBayes on HiPerGator’

3 minute read

Published:

Update on hipergator and allocating resources on dev

Hipergator moved it’s storage from ufrc to blue so the path should be changed to /blue/GROUPNAME/NAME/. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

planner

Digital Planner 2022

less than 1 minute read

Published:

Last year I created a digital planner using Keynote, since I wanted to use my iphone for keeping track of things. “Note” as a note keeping app is great but not I was looking for more organization in my schedule and reducing the clutter from my mind. I live in organized chaos so I wanted to give my mind a break.

running jobs

‘Running jobs on HiPerGator’

2 minute read

Published:

Breakdown of Slurm Script

HiPerGator moved from a PBS to Slurm(Simple Linux Utility for Resource Management), in 2015? or 2016?, not sure.
But let’s break down the sample bash script line by line , which you can download here

‘Modules on HiPerGator’

less than 1 minute read

Published:

Modules on HiPerGator

The tutorial available on UFRC website does a pretty good job explaining how to load a software for running jobs on the cluster.
Click here for Module Tutorial by UFRC After you have loaded the list of modules you want to load, you can save the modules to a default list by,

slurm

Using dev version on hipergator

2 minute read

Published:

Allocating resources on dev

Hipergator allows the users to allocate resources for running simple applications on the cluster. Please see the criteria for short testing jobs allowed on Hipergator here. Remember that the developmental version is only for testing purposes, so do not submit any job that takes a long time to run. I personally do not enjoy using it for longer runs, but simple applications which do not take too much time can be run on dev version by allocating resources and time as follows:

species tree

swap error

tidyverse

Publication Quality Figures in R

1 minute read

Published:

This tutorial is written to guide relatively new R students on how to make a publication ready figures in R. It can be daunting to figure this out on your own and look at several websites to figure out which R packages are needed,along with how to fulfill each journal’s requirement for fiures, so I am going to try to keep this short and simple. Here are a list of packages that are needed and can be easily installed from CRAN.

transfer files

Transferring files to the cluster (HiPerGator)

2 minute read

Published:

Now that you are on the cluster, let us learn some basic commands to navigate your way.First you need to know your location on the cluster. Type:

windows

Transferring files to the cluster (HiPerGator)

2 minute read

Published:

Now that you are on the cluster, let us learn some basic commands to navigate your way.First you need to know your location on the cluster. Type:

Using the cluster (HiPerGator)

1 minute read

Published:

If this is your first time using the cluster, I would advice to learn some basic bash scripting. Navigating your way through different directories and cluster would be a lot easier with basic bash commands such as pwd,cd, mkdir, ls ( Note to self: Make a post about it)