If you are attempting to install on a much older machine or on a machine where you can’t change much in the global environment due to numerous reason installing a virtual image which already has SeekDeep installed might work much better for you.

Installing with vagrant and virtualbox

back to top
SeekDeep can also be used by downloading a virtual image with it already installed. This is done with vagrant and virtualbox.

Installing vagrant and virtualbox Ubuntu

The newest vagrant is not in the Ubuntu default repositories or any ppa’s that I’m aware of so here’s how to install the deb by hand

Code

wget https://releases.hashicorp.com/vagrant/2.2.19/vagrant_2.2.19_x86_64.deb
sudo dpkg -i vagrant_2.2.19_x86_64.deb

Virtual box can be installed with the usual apt-get

Code

sudo apt-get update && sudo apt-get upgrade
sudo apt-get install virtualbox
sudo apt-get install vagrant

Installing vagrant and virtualbox with Brew

If you don’t have sudo rights or you can installing on Mac brew can also install vagrant and virtual box

Code

brew update 
brew upgrade
brew install vagrant
brew install virtualbox

Getting the SeekDeep image and set up

back to top
I would suggest making a directory to hold vagrant images. The SeekDeep Vagrantfile can be modified to mount a directory next to the directory where you downloaded the image where you can store the data you will be analyzing called SeekDeepData though analyzing data in this mounted directory is slow and not recommend. Instead you should analyze data in another directory.

Code

cd ~
mkdir vagrantImages
cd vagrantImages

#copy data that you will be analyzing into the SeekDeepData folder 
mkdir SeekDeepData
cd SeekDeepData
wget http://seekdeep.brown.edu/data/SeekDeepTutorialData/ver2_5_0/Multiplex_IT_Tutorial_Materials.tar.gz
cd ..

#create directory for the vagrant virtual image
mkdir SeekDeep
cd SeekDeep
vagrant init nickjhathaway/SeekDeep
vagrant up

Now the above will install the base image nickjhathaway/SeekDeep and start up a machine using that image. To go into that image from within the SeekDeep directory called vagrant ssh and you will ssh into the machine and SeekDeep should be already there and ready to use. There you will also see a directory in the home directory called data. This is a shared folder with the local host and will contain everything in the SeekDeepData directory. This is a dynamically shared resource between the virtual machine and the local host so changes made on either machine will instantly change in the other location.

Code

cd ~/vagrantImages/SeekDeep
vagrant ssh

Welcome to Ubuntu 20.04 LTS (GNU/Linux 5.4.0-40-generic x86_64)
....
....
....
....
vagrant@SeekDeep:~$

Code

vagrant@SeekDeep:~$ SeekDeep

SeekDeep
1) extractor
2) makeSampleDirectories
3) processClusters
4) qluster
5) sffExtractor
SeekDeepUtils
1) dryRunQualityFiltering
2) genProjectConfig
3) popClusteringViewer
4) runMultipleCommands

You can now navigate to the data directory where the data you copied into the SeekDeepData directory will be

Code

vagrant@SeekDeep:~$ ls

data

Code

vagrant@SeekDeep:~$ cd data
vagrant@SeekDeep:~$ ls

Multiplex_IT_Tutorial_Materials.tar.gz

Also calling vagrant ssh is like sshing into any machine, once you are done with your work you can just call exit to get out of the machine and the machine will continue to run until you call vagrant halt or vagrant suspend (See below for details).

Vagrant helpful tips

You can see full vagrant usage here. Below are some helpful tips.

Setting RAM and CPUs for the image

By default the SeekDeep image will be use 4 CPUs and 8GB of RAM. To change this simply edit the Vagrantfile within the SeekDeep vagrant directory. To set the RAM and CPUs add the following any where after Vagrant.configure(2) do |config| before the last end. The file is written in ruby if you are familiar with that language.

Code

....
   config.vm.provider "virtualbox" do |vb|
     vb.memory = "12288"
     vb.cpus = 8
   end
....

The amount of memory is in MB so the above would allow the machine to use 8 CPUs and 12GB of RAM.
To apply these changes to the image, first shut it down if it is running and call vagrant up again

Code

#Should be called within the directory initialized with the image you want to stop and restart
cd ~/vagrantImages/SeekDeep
#make changes to the Vagrantfile here
vagrant halt
vagrant up
vagrant ssh

Shutting down the image

There are two different ways to shut down a running vagrant virtual image using vagrant halt and vagrant suspend. These commands should be called within the directory where the image you intend to stop was initialized in. vagrant halt will cause a full shut down without saving any sort of state information where as vagrant suspend will cause vagrant to save everything that is currently happening.

Full Shut Down

vagrant halt will shut down the machine and is similar to how you normally just shut down a computer

Code

#Should be called within the directory initialized with the image you want to stop
cd ~/vagrantImages/SeekDeep
vagrant halt

==> default: Attempting graceful shutdown of VM...

To start up the image again just call vagrant up again

Code

#Should be called within the directory initialized with the image you want to start
cd ~/vagrantImages/SeekDeep
vagrant up

Bringing machine 'default' up with 'virtualbox' provider...
==> default: Checking if box 'nickjhathaway/SeekDeep' is up to date...
==> default: Clearing any previously set forwarded ports...
....
....
....

Stopping the machine will cause it to no longer eat up RAM.

Shut down, save state

To save the current state of the image use vagrant susepnd. This could end up saving a large amount of disk space as the RAM currently being used by the virtual machine will have to be saved.

Code

#Should be called within the directory initialized with the image you want to stop
cd ~/vagrantImages/SeekDeep
vagrant suspend

==> default: Saving VM state and suspending execution...

To restart a suspended image in the state saved use vagrant resume

Code

#Should be called within the directory initialized with the image you want to start
cd ~/vagrantImages/SeekDeep
vagrant resume

==> default: Resuming suspended VM...
==> default: Booting VM...
==> default: Waiting for machine to boot. This may take a few minutes...
    default: SSH address: 127.0.0.1:2200
    default: SSH username: vagrant
    default: SSH auth method: private key
    default: Warning: Connection refused. Retrying...
==> default: Machine booted and ready!

The benefit of doing this is saving the current state of the machine but it will no longer eat up RAM.

If you are attempting to install on a much older machine or on a machine where you can't change much in the global environment due to numerous reason installing a virtual image which already has SeekDeep installed might work much better for you. # Installing with vagrant and virtualbox [back to top](#TOC) SeekDeep can also be used by downloading a virtual image with it already installed. This is done with [vagrant](https://www.vagrantup.com/downloads.html) and [virtualbox](https://www.virtualbox.org/wiki/Downloads). ## Installing vagrant and virtualbox Ubuntu [back to top](#TOC) The newest vagrant is not in the Ubuntu default repositories or any ppa's that I'm aware of so here's how to install the deb by hand ```{r, engine='bash',comment="",eval=FALSE} wget https://releases.hashicorp.com/vagrant/2.2.19/vagrant_2.2.19_x86_64.deb sudo dpkg -i vagrant_2.2.19_x86_64.deb ``` Virtual box can be installed with the usual apt-get ```{r, engine='bash',comment="",eval=FALSE} sudo apt-get update && sudo apt-get upgrade sudo apt-get install virtualbox sudo apt-get install vagrant ``` ## Installing vagrant and virtualbox with Brew If you don't have sudo rights or you can installing on Mac brew can also install vagrant and virtual box ```{r, engine='bash',comment="",eval=FALSE} brew update brew upgrade brew install vagrant brew install virtualbox ``` ## Getting the SeekDeep image and set up [back to top](#TOC) I would suggest making a directory to hold vagrant images. The SeekDeep Vagrantfile can be modified to mount a directory next to the directory where you downloaded the image where you can store the data you will be analyzing called `SeekDeepData` though analyzing data in this mounted directory is slow and not recommend. Instead you should analyze data in another directory. ```{r, engine='bash',comment="",eval=FALSE} cd ~ mkdir vagrantImages cd vagrantImages #copy data that you will be analyzing into the SeekDeepData folder mkdir SeekDeepData cd SeekDeepData wget http://seekdeep.brown.edu/data/SeekDeepTutorialData/ver2_5_0/Multiplex_IT_Tutorial_Materials.tar.gz cd .. #create directory for the vagrant virtual image mkdir SeekDeep cd SeekDeep vagrant init nickjhathaway/SeekDeep vagrant up ``` Now the above will install the base image nickjhathaway/SeekDeep and start up a machine using that image. To go into that image from within the SeekDeep directory called `vagrant ssh` and you will ssh into the machine and SeekDeep should be already there and ready to use. There you will also see a directory in the home directory called data. This is a shared folder with the local host and will contain everything in the SeekDeepData directory. This is a dynamically shared resource between the virtual machine and the local host so changes made on either machine will instantly change in the other location. ```{r, engine='bash',comment="",eval=FALSE} cd ~/vagrantImages/SeekDeep vagrant ssh ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "Welcome to Ubuntu 20.04 LTS (GNU/Linux 5.4.0-40-generic x86_64) .... .... .... .... vagrant@SeekDeep:~$" ``` ```{r, engine='bash',comment="",eval=FALSE} vagrant@SeekDeep:~$ SeekDeep ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "SeekDeep 1) extractor 2) makeSampleDirectories 3) processClusters 4) qluster 5) sffExtractor SeekDeepUtils 1) dryRunQualityFiltering 2) genProjectConfig 3) popClusteringViewer 4) runMultipleCommands" ``` You can now navigate to the `data` directory where the data you copied into the `SeekDeepData` directory will be ```{r, engine='bash',comment="",eval=FALSE} vagrant@SeekDeep:~$ ls ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "data" ``` ```{r, engine='bash',comment="",eval=FALSE} vagrant@SeekDeep:~$ cd data vagrant@SeekDeep:~$ ls ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "Multiplex_IT_Tutorial_Materials.tar.gz" ``` Also calling vagrant ssh is like sshing into any machine, once you are done with your work you can just call exit to get out of the machine and the machine will continue to run until you call `vagrant halt` or `vagrant suspend` (See below for details). ## Vagrant helpful tips You can see full vagrant usage [here](https://docs.vagrantup.com/v2/). Below are some helpful tips. ### Setting RAM and CPUs for the image By default the SeekDeep image will be use 4 CPUs and 8GB of RAM. To change this simply edit the `Vagrantfile` within the SeekDeep vagrant directory. To set the RAM and CPUs add the following any where after `Vagrant.configure(2) do |config|` before the last `end`. The file is written in ruby if you are familiar with that language. ```{r, engine='ruby',comment="",eval=FALSE} .... config.vm.provider "virtualbox" do |vb| vb.memory = "12288" vb.cpus = 8 end .... ``` The amount of memory is in MB so the above would allow the machine to use 8 CPUs and 12GB of RAM. To apply these changes to the image, first shut it down if it is running and call `vagrant up` again ```{r, engine='bash',comment="",eval=FALSE} #Should be called within the directory initialized with the image you want to stop and restart cd ~/vagrantImages/SeekDeep #make changes to the Vagrantfile here vagrant halt vagrant up vagrant ssh ``` ### Shutting down the image There are two different ways to shut down a running vagrant virtual image using `vagrant halt` and `vagrant suspend`. These commands should be called within the directory where the image you intend to stop was initialized in. `vagrant halt` will cause a full shut down without saving any sort of state information where as `vagrant suspend` will cause vagrant to save everything that is currently happening. #### Full Shut Down `vagrant halt` will shut down the machine and is similar to how you normally just shut down a computer ```{r, engine='bash',comment="",eval=FALSE} #Should be called within the directory initialized with the image you want to stop cd ~/vagrantImages/SeekDeep vagrant halt ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "==> default: Attempting graceful shutdown of VM..." ``` To start up the image again just call `vagrant up` again ```{r, engine='bash',comment="",eval=FALSE} #Should be called within the directory initialized with the image you want to start cd ~/vagrantImages/SeekDeep vagrant up ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "Bringing machine 'default' up with 'virtualbox' provider... ==> default: Checking if box 'nickjhathaway/SeekDeep' is up to date... ==> default: Clearing any previously set forwarded ports... .... .... ...." ``` Stopping the machine will cause it to no longer eat up RAM. #### Shut down, save state To save the current state of the image use `vagrant susepnd`. This could end up saving a large amount of disk space as the RAM currently being used by the virtual machine will have to be saved. ```{r, engine='bash',comment="",eval=FALSE} #Should be called within the directory initialized with the image you want to stop cd ~/vagrantImages/SeekDeep vagrant suspend ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "==> default: Saving VM state and suspending execution..." ``` To restart a suspended image in the state saved use `vagrant resume` ```{r, engine='bash',comment="",eval=FALSE} #Should be called within the directory initialized with the image you want to start cd ~/vagrantImages/SeekDeep vagrant resume ``` ```{r, engine='bash',comment="",eval=TRUE, echo =FALSE} echo "==> default: Resuming suspended VM... ==> default: Booting VM... ==> default: Waiting for machine to boot. This may take a few minutes... default: SSH address: 127.0.0.1:2200 default: SSH username: vagrant default: SSH auth method: private key default: Warning: Connection refused. Retrying... ==> default: Machine booted and ready!" ``` The benefit of doing this is saving the current state of the machine but it will no longer eat up RAM.