MIPWrangler is one command line program that contains several programs within that all combined together make up the MIPWrangler targeted molecular inversion probe (MIP) sequencing analysis pipeline. Currently installs only MAC, Ubuntu, and other UNIX based systems is supported.
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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.
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.
#install homebrew
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
#run brew doctor
brew doctorYou 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
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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.
To install cmake the following brew commands can be used
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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. MIPWrangler requires > g++-5 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 MIPWrangler than gcc.
#configure and choose compilers
#no arguments assumes clang++ or whatever environmental CC and CXX are set to
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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 MIPWrangler 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.
# will install dependent libaries in a folder called external
./setup.py --compfile compfile.mk --outMakefile makefile-common.mkThis 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.
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If the setup.py was able to install everything, next is to make MIPWrangler itself which takes a simple make command and will compile MIPWrangler in a directory called bin/ in the MIPWrangler directory
To use more cores to speed up make use -j, below would use 4 cores
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.
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To call MIPWrangler from the command line it will need to be called either with it’s full name or adding the bin directory in the MIPWrangler 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
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A lot of the flags in MIPWrangler 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 MIPWrangler. 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)
muscle is a third party tools that MIPWrangler calls from it’s sequence viewer and can be installed via the following
To get a list of commands that MIPWrangler can call simply call it without any arguments
Version 1.0.0
Programs
Use MIPWrangler [PROGRAM] --help to see more details about each program
Commands are not case sensitive
MIPWrangler
mipsterMipExplorer
1) mipsAgainstHaplotypes
2) setUpViewMipsOnGenome
3) viewMipsOnGenome
mipsterMipTester
1) callMircosateliteSizes
mipsterServer
1) mav
2) mipAnalysisServerSetUp
MIPWranglerAnalysis
01) mipBarcodeCorrectionMultiple
02) mipClusteringMultiple
03) mipCorrectForContamWithSameBarcodesMultiple
04) mipPopulationClusteringMultiple
05) mipSetupAndExtractByArm
06) mipSkipBarcodeCorrectionMultiple
MIPWranglerSetUp
1) checkDirectoryStructure
2) cloneAnalysisDirectory
MIPWranglerSim
1) createArmFastaFiles
2) extractMipCaptureSequence
3) mipSimSetup
4) searchForArms
5) simMips
MIPWranglerUtils
01) createExtArmFastas
02) createLigArmFastas
03) createPrimerFileFromArmFile
04) mipFastasToSeqTable
05) processMipOverlapGraph
06) processMipOverlapGraphSingle
07) rearmTargetsAndCombine
08) typeFinalHaplotypes
09) writeOutPossibleHaplotypes