SeekDeep

SeekDeep is one command line program that contains several programs within that all combined together make up the SeekDeep targeted sequencing analysis pipeline. Currently installs only MAC, Ubuntu, and other UNIX based systems is supported.

Downloading code

back to top
Source code for the program is hosted at github and can be downloaded by either using git (recommended) or by downloading a compressed folder of the code
The recommended approach is to use git to clone the repository for the code because this is the easiest way to keep the code up to date.

Code

cd ~
git clone https://github.com/bailey-lab/SeekDeep
cd SeekDeep

Or downloading compressed folder, latest version is v3.0.1, this is not recommended as this will make it harder to keep the code up to date

Code

cd ~
wget https://github.com/bailey-lab/SeekDeep/archive/v3.0.1.tar.gz
tar zxvf v3.0.1.tar.gz 
cd SeekDeep-v3.0.1/

Installing Dependencies

To install extra packages on Mac OS X the easier way is to use a package manager like brew (recommended) or macports. Instructions on brew found here.

Code

#install homebrew
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
#run brew doctor 
brew doctor

You will most likely need to install Xcode as well which is free via the app store and then you also need to install the Xcode command line tools

Code

xcode-select --install

Compliers

back to top
You need to have either clang or g++ installed. For mac the easiest is to just use the mac packaged clang package ### Clang back to top
Mac comes packaged with clang though you might have to install Xcode to get it to be accessible. Xcode is free and can be download via the app store though you might also have to make sure the Xcode command line tools are also installed.

Code

xcode-select --install

Libraries

To install cmake the following brew commands can be used

Code

brew update
brew upgrade
brew install cmake

Configuring

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Once code has been downloaded it needs to be compiled but first come dependencies have to be downloaded and a compiler has to be chosen. SeekDeep requires > g++-10 or clang++-3.8 to be compiled. It has been extensively tested on clang++ and therefore is more likely to compile without problems using clang++. clang++ has also been demonstrated to install a faster final executable for SeekDeep than gcc.

Code

#configure and choose compilers
#no arguments assumes clang++ or whatever environmental CC and CXX are set to 
./configure.py

Installing Further Dependencies Libraries

back to top
Calling configure will create a file called compfile.mk which will contain info on the libraries needed and what compilers to use, this is give to setup.py to download the libraries SeekDeep relay on. This may take some time especially if being done on a machine that doesn’t have many cores. Some of these dependencies might be worked out in future releases making install easier.

Code

# will install dependent libaries in a folder called external
./setup.py --compfile compfile.mk --outMakefile makefile-common.mk

This command should report on whether anything failed to install, if this does happen, contact Nick Hathaway at Nicholas.Hathaway@umassmed.edu to complain to him his install is annoying and therefore failing, and send along any errors messages that can be found.

Compiling

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If the setup.py was able to install everything, next is to make SeekDeep itself which takes a simple make command and will compile SeekDeep in a directory called bin/ in the SeekDeep directory

Code

make

To use more cores to speed up make use -j, below would use 4 cores

Code

make -j 4

Again if this fails to compile, complain to Nick (Nicholas.Hathaway@umassmed.edu) that he should get his act together to make this an easier install.

Adding SeekDeep to path

back to top
To call SeekDeep from the command line it will need to be called either with it’s full name or adding the bin directory in the SeekDeep directory to your environmental path. This is done by modifying your ~/.profile file (on MAC it’s ~/.bash_profile). Also this won’t take effect until this file is sourced either on your next log in or by called source ~/.profile

Code

#add the following to your ~/.bash_profile and replace $HOME/ with the path where SeekDeep was downloaded
export PATH=$HOME/SeekDeep/bin/:$PATH

Adding auto flag completion

back to top
A lot of the flags in SeekDeep can be long and annoying to type in so and auto flag completion has been added in folder called bash_completion.d in a file called SeekDeep. The content of this file should be added to ~/.bash_completion though your shell environment must already be set up for bash completion which is true for most Ubuntu machines but not always of Macs but brew can help set it up. There is also a command in ./setup.py that will add this to .bash_completion for you (it simply does what was said above and puts the contents of the file in bashCompletes to ~/.bash_completion)

Code

brew install bash-completion

Code

./setup.py --addBashCompletion

Adding additional tools.

muscle is a third party tools that SeekDeep call and should be installed as

Code

#add other tools 
./setup.py --libs muscle:3.8.31 --symlinkBin --overWrite

Calling SeekDeep commands

To get a list of commands that SeekDeep can call simply call it without any arguments

Code

SeekDeep

Version 3.0.2-dev
Programs
Use SeekDeep [PROGRAM] --help to see more details about each program
Commands are not case sensitive
SeekDeep
1) extractor
2) extractorByKmerMatching
3) extractorPairedEnd
4) kluster
5) makeSampleDirectories
6) processClusters
7) qluster
SeekDeepServer
1) genProjectConfig
2) popClusteringViewer
SeekDeepUtils
01) benchmarkControlMixturesOnProcessedClustersDir
02) benchmarkMultiTarAmpControlMixtures
03) benchmarkTarAmpControlMixtures
04) combineBasicResultsFiles
05) deRepPopClusDir
06) dryRunQualityFiltering
07) gatherInfoOnTargetedAmpliconSeqFile
08) genTargetInfoFromGenomes
09) getPossibleSampleNamesFromRawInput
10) primersToFasta
11) rBind
12) replaceUnderscores
13) runMultipleCommands
14) SampleBarcodeFileToSeekDeepInput
15) setupTarAmpAnalysis
16) variantCallOnSeqAndProtein

Then to call a sub-command just type it’s name after SeekDeep, and without adding arguments will automatically print it’s help message

Code

SeekDeep qluster

#or with -help/-h 
SeekDeep qluster --help

Also the commands and flags of SeekDeep are not case sensitive so all the below would work

Code

SeekDeep qluster --help 
SeekDeep qluster --HELP
SeekDeep qluster --HeLP
SeekDeep qluster --HeLp
SeekDeep QLUSTER --HeLP
SeekDeep qluster --HeLp
SeekDeep qlUstEr --HeLp

# SeekDeep SeekDeep is one command line program that contains several programs within that all combined together make up the SeekDeep targeted sequencing analysis pipeline. Currently installs only MAC, Ubuntu, and other UNIX based systems is supported. # Downloading code [back to top](#TOC) Source code for the program is hosted at [github](https://github.com/bailey-lab/SeekDeep) and can be downloaded by either using git (recommended) or by downloading a compressed folder of the code The recommended approach is to use git to clone the repository for the code because this is the easiest way to keep the code up to date. ```{r downloading-git, echo=T, eval=FALSE, engine='bash'} cd ~ git clone https://github.com/bailey-lab/SeekDeep cd SeekDeep ``` **Or** downloading compressed folder, latest version is v3.0.1, this is not recommended as this will make it harder to keep the code up to date ```{r downloading-tar, echo=T, eval=FALSE, engine='bash'} cd ~ wget https://github.com/bailey-lab/SeekDeep/archive/v3.0.1.tar.gz tar zxvf v3.0.1.tar.gz cd SeekDeep-v3.0.1/ ``` # Installing Dependencies [back to top](#TOC) To install extra packages on Mac OS X the easier way is to use a package manager like brew (recommended) or macports. Instructions on brew found [here](http://brew.sh/). ```{r , echo=T, eval=FALSE, engine='bash'} #install homebrew ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" #run brew doctor brew doctor ``` You will most likely need to install Xcode as well which is free via the app store and then you also need to install the Xcode command line tools ```{r , echo=T, eval=FALSE, engine='bash'} xcode-select --install ``` ## Compliers [back to top](#TOC) You need to have either clang or g++ installed. For mac the easiest is to just use the mac packaged clang package ### Clang [back to top](#TOC) Mac comes packaged with clang though you might have to install Xcode to get it to be accessible. Xcode is free and can be download via the app store though you might also have to make sure the Xcode command line tools are also installed. ```{r , echo=T, eval=FALSE, engine='bash'} xcode-select --install ``` ### Libraries To install cmake the following brew commands can be used ```{r , echo=T, eval=FALSE, engine='bash'} brew update brew upgrade brew install cmake ``` # Configuring [back to top](#TOC) Once code has been downloaded it needs to be compiled but first come dependencies have to be downloaded and a compiler has to be chosen. SeekDeep requires > g++-10 or clang++-3.8 to be compiled. It has been extensively tested on clang++ and therefore is more likely to compile without problems using clang++. clang++ has also been demonstrated to install a faster final executable for SeekDeep than gcc. ```{r configuring, echo=T, eval=FALSE, engine='bash'} #configure and choose compilers #no arguments assumes clang++ or whatever environmental CC and CXX are set to ./configure.py ``` ## Installing Further Dependencies Libraries [back to top](#TOC) Calling configure will create a file called compfile.mk which will contain info on the libraries needed and what compilers to use, this is give to setup.py to download the libraries SeekDeep relay on. This may take some time especially if being done on a machine that doesn't have many cores. Some of these dependencies might be worked out in future releases making install easier. ```{r install_dependencies, echo=T, eval=FALSE, engine='bash'} # will install dependent libaries in a folder called external ./setup.py --compfile compfile.mk --outMakefile makefile-common.mk ``` This command should report on whether anything failed to install, if this does happen, contact Nick Hathaway at Nicholas.Hathaway@umassmed.edu to complain to him his install is annoying and therefore failing, and send along any errors messages that can be found. # Compiling [back to top](#TOC) If the setup.py was able to install everything, next is to make SeekDeep itself which takes a simple `make` command and will compile SeekDeep in a directory called bin/ in the SeekDeep directory ```{r compiling, echo=T, eval=FALSE, engine='bash'} make ``` To use more cores to speed up make use -j, below would use 4 cores ```{r compiling-threaded, echo=T, eval=FALSE, engine='bash'} make -j 4 ``` Again if this fails to compile, complain to Nick (Nicholas.Hathaway@umassmed.edu) that he should get his act together to make this an easier install. # Adding SeekDeep to path [back to top](#TOC) To call SeekDeep from the command line it will need to be called either with it's full name or adding the bin directory in the SeekDeep directory to your environmental path. This is done by modifying your ~/.profile file (on MAC it's ~/.bash_profile). Also this won't take effect until this file is sourced either on your next log in or by called `source ~/.profile` ```{r adding_to_path, echo=T, eval=FALSE, engine='bash'} #add the following to your ~/.bash_profile and replace $HOME/ with the path where SeekDeep was downloaded export PATH=$HOME/SeekDeep/bin/:$PATH ``` # Adding auto flag completion [back to top](#TOC) A lot of the flags in **SeekDeep** can be long and annoying to type in so and auto flag completion has been added in folder called bash_completion.d in a file called SeekDeep. The content of this file should be added to ~/.bash_completion though your shell environment must already be set up for bash completion which is true for most Ubuntu machines but not always of Macs but brew can help set it up. There is also a command in `./setup.py` that will add this to .bash_completion for you (it simply does what was said above and puts the contents of the file in bashCompletes to ~/.bash_completion) ```{r auto_complete 1 , echo=T, eval=FALSE, engine='bash'} brew install bash-completion ``` ```{r auto_complete 2, echo=T, eval=FALSE, engine='bash'} ./setup.py --addBashCompletion ``` # Adding additional tools. muscle is a third party tools that SeekDeep call and should be installed as ```{r, echo=T, eval=FALSE, engine='bash'} #add other tools ./setup.py --libs muscle:3.8.31 --symlinkBin --overWrite ``` # Calling SeekDeep commands To get a list of commands that SeekDeep can call simply call it without any arguments ```{r callingSeekDeep, echo=T, eval=FALSE, engine='bash'} SeekDeep ``` ```{r, echo=F, eval=T, engine='bash'} SeekDeep ``` Then to call a sub-command just type it's name after SeekDeep, and without adding arguments will automatically print it's help message ```{r , echo=T, eval=FALSE, engine='bash'} SeekDeep qluster #or with -help/-h SeekDeep qluster --help ``` ```{r, echo=F, eval=F, engine='bash'} SeekDeep qluster --help | gsed -r "s/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[m|K]//g" | head -15 echo .... ``` Also the commands and flags of SeekDeep are not case sensitive so all the below would work ```{r, engine='bash',comment="",eval=FALSE} SeekDeep qluster --help SeekDeep qluster --HELP SeekDeep qluster --HeLP SeekDeep qluster --HeLp SeekDeep QLUSTER --HeLP SeekDeep qluster --HeLp SeekDeep qlUstEr --HeLp ```