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| -rw-r--r-- | doc/index.markdown | 32 | ||||
| -rw-r--r-- | doc/install.markdown | 47 |
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diff --git a/doc/README.markdown b/doc/README.markdown index 82004aa..1aad66b 100644 --- a/doc/README.markdown +++ b/doc/README.markdown @@ -1,47 +1,32 @@ -# How Can I Install The Quikr Utility? # -To use Quikr there are several prerequisites. - -## Requirements ## -+ Mac OS X 10.6.8 or GNU/Linux -+ 4Gb of RAM minimum. Absolutely neccessary. -+ gcc that supports OpenMP - -### Python Requirements ### -+ Python 2.7 -+ Scipy -+ Numpy -+ BioPython - -### Mac Requirements ### -+ Mac OS X 10.6.8 (what we have tested) -+ GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation) -+ OCaml compiler mlton -+ OpenMP libraries (libgomp, usually comes with gcc) - -### Linux Requirements ### -+ GCC 4.7 or newer -+ OCaml compiler mlton -+ OpenMP libraries (libgomp, usually comes with gcc) - -We also have a Quikr implementation in Matlab so that you can easily integrate -Quikr into your custom programs and scripts. - -### Installation ### -Our Quikr code is available on our sourceforge download page: - -[http://sourceforge.net/projects/quikr/](sourceforge project page) - -Our development GIT repository is available here: - -[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/) - -To install quikr, download our project and in the folder run: - - make - sudo make install - -This will install the quikr, quikr\_train and multifasta\_to\_otu utilities. -To install the python scripts and module systemwide, run - - make python - sudo make install_python +# Quikr # +This is the homepage for quikr. + +## What is Quikr ## +Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that +utilizes sparsity promoting ideas from the field of compressed sensing to +reconstruct the composition of a bacterial community (when the input data is +454-like pyrosequencing data). This extremely fast method comes with a default +training database but can be custom trained. Typically reconstruction is +accurate down to the genus level. + + +## How Do I Install Quikr ## +Please read the directions on the [installation page](install.markdown). + +## How Do I use Quikr ## +We have several ways to use quikr. Quikr is first and formost a command +line utility, but we also provide python and matlab scripts. + ++ [Command Line Utilities](cli.markdown) ++ [Matlab documentation](matlab.markdown) ++ [Python documentation](python.markdown) + +## Contact ## +For issues with the quikr software, contact gailro@gmail.com + +## Contributors ## ++ David Koslicki ++ Simon Foucart ++ Gail Rosen ++ Calvin Morrison ++ Jean-Luc Bouchot diff --git a/doc/index.markdown b/doc/index.markdown deleted file mode 100644 index 1aad66b..0000000 --- a/doc/index.markdown +++ /dev/null @@ -1,32 +0,0 @@ -# Quikr # -This is the homepage for quikr. - -## What is Quikr ## -Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that -utilizes sparsity promoting ideas from the field of compressed sensing to -reconstruct the composition of a bacterial community (when the input data is -454-like pyrosequencing data). This extremely fast method comes with a default -training database but can be custom trained. Typically reconstruction is -accurate down to the genus level. - - -## How Do I Install Quikr ## -Please read the directions on the [installation page](install.markdown). - -## How Do I use Quikr ## -We have several ways to use quikr. Quikr is first and formost a command -line utility, but we also provide python and matlab scripts. - -+ [Command Line Utilities](cli.markdown) -+ [Matlab documentation](matlab.markdown) -+ [Python documentation](python.markdown) - -## Contact ## -For issues with the quikr software, contact gailro@gmail.com - -## Contributors ## -+ David Koslicki -+ Simon Foucart -+ Gail Rosen -+ Calvin Morrison -+ Jean-Luc Bouchot diff --git a/doc/install.markdown b/doc/install.markdown new file mode 100644 index 0000000..82004aa --- /dev/null +++ b/doc/install.markdown @@ -0,0 +1,47 @@ +# How Can I Install The Quikr Utility? # +To use Quikr there are several prerequisites. + +## Requirements ## ++ Mac OS X 10.6.8 or GNU/Linux ++ 4Gb of RAM minimum. Absolutely neccessary. ++ gcc that supports OpenMP + +### Python Requirements ### ++ Python 2.7 ++ Scipy ++ Numpy ++ BioPython + +### Mac Requirements ### ++ Mac OS X 10.6.8 (what we have tested) ++ GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation) ++ OCaml compiler mlton ++ OpenMP libraries (libgomp, usually comes with gcc) + +### Linux Requirements ### ++ GCC 4.7 or newer ++ OCaml compiler mlton ++ OpenMP libraries (libgomp, usually comes with gcc) + +We also have a Quikr implementation in Matlab so that you can easily integrate +Quikr into your custom programs and scripts. + +### Installation ### +Our Quikr code is available on our sourceforge download page: + +[http://sourceforge.net/projects/quikr/](sourceforge project page) + +Our development GIT repository is available here: + +[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/) + +To install quikr, download our project and in the folder run: + + make + sudo make install + +This will install the quikr, quikr\_train and multifasta\_to\_otu utilities. +To install the python scripts and module systemwide, run + + make python + sudo make install_python |