popClusteringViewer’s Purpose

popClusteringViewer is used to view the final results of the SeekDeep targeted amplicon sequencing analysis pipeline that is created by SeekDeep processClusters. It sets up a local HTTP server for an interactive interface for viewing all results. To run it needs the name of the directory created by SeekDeep processClusters and the name of the directory of javascript and html files downloaded with SeekDeep

Getting usage command line

Giving the -help flag will get information on requirements for running SeekDeep popClusteringViewer

Code

SeekDeep popClusteringViewer --help

SeekDeep popClusteringViewer
           Required Options
            Miscellaneous
      --configDir   Name of the Master Result Directory; required; default=; (boost::filesystem::path)
           Optional Options
            Miscellaneous
    --bindAddress   Address to bind to, defaults to 127.0.0.1 (localhost); default=127.0.0.1; (std::string)
          --debug   Debug; default=false; (bool)
           --name   Name of root of the server; default=pcv; (std::string)
           --port   Port Number to Serve On; default=9881; (uint32_t)
--resourceDirName   Name of the resource Directory where the js and html is located; default=/Users/nick/hathawayTesting/external/local/SeekDeep/develop/SeekDeep/etc/serverResources; (boost::filesystem::path)
  --seqServerCore   Name of the seqServerCore Directory where the js and html for the core seqServer code is located; default=/Users/nick/hathawayTesting/external/local/seqServer/develop/seqServer/etc/resources/seqServerCore; (boost::filesystem::path)
     --verbose,-v   Verbose; default=false; (bool)
     --workingDir   The working directory to store temporary files; default=/tmp/; (boost::filesystem::path)
             Help Options
...
...

Also all flags in SeekDeep are case insensitive and so all the following would have the same results

Code

SeekDeep popClusteringViewer --help 
SeekDeep popClusteringViewer --HELP
SeekDeep POPClusteringViewer --HeLP
SeekDeep popClusteringViewer --HeLp
SeekDeep POPCLUSTERINGVIEWER --HeLP
SeekDeep PopClusteringViewer --HeLp
SeekDeep popClusteringVIEWER --HeLp

Examples

General Usage

SeekDeep popClusteringViewer needs 1 flag to run, --configDir.
* –configDir: This is a directory with configure files created by SeekDeep genProjectConfig, see below

SeekDeep genProjectConfig

–mainDir: This is the output directory created by SeekDeep processClusters
–projectName: This can be any name to give to your project
–shortName: This is a shorter name for the project, this is used in the url for the hosting so should be short and contain only letters and numbers, will default to just --projectName
–out: By default SeekDeep genProjectConfig will create a *.config file where the prefix is the name given to --shortName, use --overWrite to overWrite it

Code

SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName mpn --overWrite

You can give a file or redirect the output to a file

Code

SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName mpn --out outfile.config --overWrite

General Usage contin.

You need to create a directory with configuration files create by SeekDeep genProjectConfig, most of the time you might just have one but if you have multiple clustering projects you can host multiple projects at once.

Code

mkdir configs
SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName mpn --out configs/outfile.config

Calling this command will print out a address that the HTTP server is being hosted at, copy this address into a browser to start using the server

Code

SeekDeep popClusteringViewer --configDir configs

localhost:9881/pcv

Also viewing extraction data

Code


SeekDeep genProjectConfig  --mainDir finalResultsDir --projectName myProjectName --shortName myProjectName --extractionDir extractionFiles --indexToDir indexToFilename.tab.txt --sampNames ../../sampleNames.tab.txt --out configs/out.config
SeekDeep popClusteringViewer --configDir configs

Changing port

If you have several servers running or something is already running at the default port you may have to change the port number to get the server running, this can be done with the -port flag

Code

SeekDeep popClusteringViewer --configDir configs

localhost:9881/pcv
system: Address already in use

Code

SeekDeep popClusteringViewer --configDir configs -port 9882

localhost:9882/pcv

:::{.callout-note} # popClusteringViewer's Purpose popClusteringViewer is used to view the final results of the SeekDeep targeted amplicon sequencing analysis pipeline that is created by [SeekDeep processClusters](processClusters_usage.html). It sets up a local HTTP server for an interactive interface for viewing all results. To run it needs the name of the directory created by [SeekDeep processClusters](processClusters_usage.html) and the name of the directory of javascript and html files downloaded with SeekDeep ::: # Getting usage command line Giving the -help flag will get information on requirements for running **SeekDeep popClusteringViewer** ```{r, engine='bash',comment="",eval=FALSE} SeekDeep popClusteringViewer --help ``` ```{r, engine='bash',comment="",highlight=TRUE, echo=FALSE} SeekDeep popClusteringViewer --help | gsed -r "s/\x1B\[([0-9]{1,3}((;[0-9]{1,3})*)?)?[m|K]//g" | head -15 echo ... echo ... ``` Also all flags in SeekDeep are case insensitive and so all the following would have the same results ```{r, engine='bash',comment="",eval=FALSE} SeekDeep popClusteringViewer --help SeekDeep popClusteringViewer --HELP SeekDeep POPClusteringViewer --HeLP SeekDeep popClusteringViewer --HeLp SeekDeep POPCLUSTERINGVIEWER --HeLP SeekDeep PopClusteringViewer --HeLp SeekDeep popClusteringVIEWER --HeLp ``` ```{r, engine='bash',comment="",eval=FALSE, echo=FALSE} SeekDeep popClusteringViewer --getFlags ``` ```{r, engine='bash',comment="",highlight=TRUE, eval=FALSE, echo=FALSE} SeekDeep popClusteringViewer --getFlags | gsed -r "s/\x1B\[([0-9]{1,3}((;[0-9]{1,3})*)?)?[m|K]//g" | head -20 echo ... echo ... ``` # Examples ## General Usage **SeekDeep popClusteringViewer** needs 1 flag to run, `--configDir`. * **--configDir**: This is a directory with configure files created by **SeekDeep genProjectConfig**, see below ### SeekDeep genProjectConfig * **--mainDir**: This is the output directory created by [SeekDeep processClusters](processClusters_usage.html) * **--projectName**: This can be any name to give to your project * **--shortName**: This is a shorter name for the project, this is used in the url for the hosting so should be short and contain only letters and numbers, will default to just `--projectName` * **--out**: By default `SeekDeep genProjectConfig` will create a *.config file where the prefix is the name given to `--shortName`, use `--overWrite` to overWrite it ```{r, engine='bash',comment="",eval=T} SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName mpn --overWrite ``` You can give a file or redirect the output to a file ```{r, engine='bash',comment="",eval=T} SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName mpn --out outfile.config --overWrite ``` ## General Usage contin. You need to create a directory with configuration files create by **SeekDeep genProjectConfig**, most of the time you might just have one but if you have multiple clustering projects you can host multiple projects at once. ```{r, engine='bash',comment="",eval=F} mkdir configs SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName mpn --out configs/outfile.config ``` Calling this command will print out a address that the HTTP server is being hosted at, copy this address into a browser to start using the server ```{r, engine='bash',comment="",eval=FALSE} SeekDeep popClusteringViewer --configDir configs ``` ```{r, engine='bash',comment="",highlight=TRUE, echo=FALSE} echo localhost:9881/pcv ``` ## Also viewing extraction data **** ```{r, engine='bash',comment="",eval=FALSE, echo=T} SeekDeep genProjectConfig --mainDir finalResultsDir --projectName myProjectName --shortName myProjectName --extractionDir extractionFiles --indexToDir indexToFilename.tab.txt --sampNames ../../sampleNames.tab.txt --out configs/out.config SeekDeep popClusteringViewer --configDir configs ``` ```{r, engine='bash',comment="",highlight=TRUE, echo=FALSE, eval = FALSE} echo localhost:9881/pcv ``` ## Changing port If you have several servers running or something is already running at the default port you may have to change the port number to get the server running, this can be done with the `-port` flag ```{r, engine='bash',comment="",eval=FALSE} SeekDeep popClusteringViewer --configDir configs ``` ```{r, engine='bash',comment="",highlight=TRUE, echo=FALSE} echo localhost:9881/pcv echo system: Address already in use ``` ```{r, engine='bash',comment="",eval=FALSE} SeekDeep popClusteringViewer --configDir configs -port 9882 ``` ```{r, engine='bash',comment="",highlight=TRUE, echo=FALSE} echo localhost:9882/pcv ```