From 4cab49ac3934a8fa568c7aee8484bd710f83c4e3 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Mon, 24 Mar 2014 17:20:14 -0400 Subject: update documentation --- doc/.cli.markdown.swo | Bin 0 -> 16384 bytes doc/.cli.markdown.swp | Bin 0 -> 16384 bytes doc/.install.markdown.swo | Bin 0 -> 12288 bytes doc/.install.markdown.swp | Bin 0 -> 12288 bytes doc/.matlab.markdown.swp | Bin 0 -> 16384 bytes doc/install.markdown | 7 ++++--- doc/matlab.markdown | 7 ------- doc/python.markdown | 3 +++ 8 files changed, 7 insertions(+), 10 deletions(-) create mode 100644 doc/.cli.markdown.swo create mode 100644 doc/.cli.markdown.swp create mode 100644 doc/.install.markdown.swo create mode 100644 doc/.install.markdown.swp create mode 100644 doc/.matlab.markdown.swp (limited to 'doc') diff --git a/doc/.cli.markdown.swo b/doc/.cli.markdown.swo new file mode 100644 index 0000000..cb4d4a8 Binary files /dev/null and b/doc/.cli.markdown.swo differ diff --git a/doc/.cli.markdown.swp b/doc/.cli.markdown.swp new file mode 100644 index 0000000..428a3b6 Binary files /dev/null and b/doc/.cli.markdown.swp differ diff --git a/doc/.install.markdown.swo b/doc/.install.markdown.swo new file mode 100644 index 0000000..94f5651 Binary files /dev/null and b/doc/.install.markdown.swo differ diff --git a/doc/.install.markdown.swp b/doc/.install.markdown.swp new file mode 100644 index 0000000..c676c32 Binary files /dev/null and b/doc/.install.markdown.swp differ diff --git a/doc/.matlab.markdown.swp b/doc/.matlab.markdown.swp new file mode 100644 index 0000000..c2e5b26 Binary files /dev/null and b/doc/.matlab.markdown.swp differ diff --git a/doc/install.markdown b/doc/install.markdown index eb0e8ce..3308f83 100644 --- a/doc/install.markdown +++ b/doc/install.markdown @@ -5,23 +5,24 @@ To use Quikr there are several prerequisites. + Mac OS X 10.6.8 or GNU/Linux + 4Gb of RAM minimum. Absolutely neccessary. + gcc that supports OpenMP -+ mlton the Standard-ML compiler ### Python Requirements ### +*the python version is out of date* + Python 2.7+ + Scipy + Numpy + BioPython +### Matlab Requrements ### ++ [dna\_utils](http://github.com/EESI/dna-utils/) must be installed + ### Mac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) -+ mlton the Standard-ML compiler + 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 diff --git a/doc/matlab.markdown b/doc/matlab.markdown index 09b0103..87a3a4d 100644 --- a/doc/matlab.markdown +++ b/doc/matlab.markdown @@ -2,13 +2,6 @@ The Quikr implementation works in Matlab and also works in Octave, but the Octave version will run much slower. -You will need to install the generate_kmers tool into your $PATH (eg /usr/bin/) -this file is available in the src/python/ directory. If you use make to install -the quikr project, it will already be installed. To test this you can run: - - which generate_kmers - - ## Quikr Example ## This is an example of how to run Quikr. Before you try the example please make make sure that you are in the quikr's matlab directory (src/matlab/): diff --git a/doc/python.markdown b/doc/python.markdown index df086d8..cbc59d1 100644 --- a/doc/python.markdown +++ b/doc/python.markdown @@ -1,3 +1,5 @@ +*The python version is outdated. do not use! It is only here for historical purposes!* + # Python Documentation # The python version comes with scripts that can be used like the regular quikr program, and also a module called quikr so integration with python scripts @@ -12,6 +14,7 @@ If you want to use our quikr module, run help on the module: >>> import quikr >>> help(quikr) + ## Python Cannot Find XYZ ## Ensure that you have Python 2.7, Scipy, Numpy, and BIOpython installed -- cgit v1.2.3