A public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data contained in .fsa or .hid files using an independently derived mathematically-based sizing algorithm. OSIRIS currently supports ABI capillary analytical platforms and numerous commercially available marker kits including all CODIS-compliant kits as well as those favored by biomedical laboratories.
- Most of the requirements are included with OSIRIS, except for wxwidgets. These were built with multithreading but not DLL, i.e.
/MTas opposed to/MDwith a few modifications. - VC++ 2010 Version 10 - In visual C++, see
Help->About Microsoft Visual Studio), it should be 10 or later to build OSIRIS. - wxWidgets (http://www.wxwidgets.org/)
libxml2,libxsltandlibiconvare included with the source code with Header files for all three libraries for MC VC++, used to replace the corresponding header files in the distribution.- Modification (already done) to these libraries are:
- In
libxslt-1.1.26/libexslt, modifiedlibexslt.hand changed#include <win32config.h>to#include <libxslt/win32config.h> - Removed all occurrences of
#include <win32config.h>from all other\*.c,\*.hfiles and made sure that#include "libexslt/libexslt.h"is present. - Created VC++ projects.
- In
- Download wxWidgets at http://wxwidgets.org/downloads/, either the ZIP or 7z download.
- Download the source code for OSIRIS version 2.5 (or 2.4 or later) from Github (Version 2.3 requires an older version of
wxWidgets). Or select the version from theBranchpulldown on the left side of the web page and selectDownload ZIPfrom the right side.
- Create a new folder, (for example
wxWidgets-3.0.2) and unpack the contents of the zip file there. - Set the environment variable
WXHOME, to the folder containing wxWidgets 3.0.2 (This is done in Control Panel, search for "environment"). - There should exist
%WXHOME%\includeand%WXHOME%\lib. - Go to the wxWidgets
buildfolder, thenmsw. - Select the appropriate solution
.slnfile for your version of Visual C++. - Build in Visual C++ for "Release" and
Win32and optionally forDebugandWin32. Both can coexist in the same directory structure.
- OSIRIS is built with Microsoft Visual C++ from Microsoft Visual Studio 2010 Professional. Use of a newer version of Visual C++ may result in compiler errors.
- It is important that the Visual C++ environment is started after setting
WXHOMEin the environment. - Make sure you are building for
Releaseand notDebug. - Unpack the zip file and go to the
osirisfolder. - Open the solution file,
osirisAll.slnwith Visual C++ 2010 (or later). - Select
ReleaseandWin32in the toolbar or from the menubar:Build->Configuration Manager - Build the solution: From the menubar:
Build->Rebuild Solution(Optional - If you built wxWidgets for "Debug" you can also build OSIRIS for "Debug" however it recommended that you copy the directory structure of an OSIRIS installation to OsirisAnalysis/Debug except forOsirisAnalysis.exe).
- After building OSIRIS, Run the perl script
.\ZipPerl\MakeZip.pl - It will set up the directory structure in
.\ZipPerl\Osirisand create a.zipfile. - If you want to create the directory structure without a zip file, then modify one line of code near the beginning of
MakeZip.pland changemy $NO_ZIP_FILE = 0;tomy $NO_ZIP_FILE = 1; - The directory structure will be in
.\ZipPerl\Osirisand can be moved.
- Mac OS X 10.9 to 10.10 build.
- Unix command line.
- Mac OS X Developer tools - try
gcc --versionto see if you havegccavailable from the tools.
- Download the source code for OSIRIS version 2.6 and unzip it to
osirisdirectory. - Download wxWidgets 3.0.2 at http://wxwidgets.org/downloads/,
Source for Linux, OS X, etc.(Current).
- Unpack the download to a new directory:
tar tvf wxWidgets-3.0.2.tar.bz2. This will create a directory with the wxWidget source code likewxWidgets-3.0.2 - Change into the directory:
cd wxWidgets-3.0.2 - Create a new directory,
build-cocoa:mkdir build-cocoa - Change into the directory:
cd build-cocoa - In
osirisdirectory, copyosiris/osiris/build-osx/config.shtowxWidgets-3.0.2/build-cocoa:cp /path/to/osiris/osiris/build-osx/config.sh . - Run the newly copied
config.sh:sh config.sh- When finished, the output will be in the file
build_log.txt - Make sure there are no error messages at the end of the file.
- When finished, the output will be in the file
- Install
wxWidgets:make install** The default installation location from the build script is~/local/wxRelease(where~represents the user's home directory).- Make sure that
~/local/wxReleasehas four subdirectories:bin,include,lib,share - Set the environment variation for wxWidgets:
export WXHOME=~/local/wxRelease
- Make sure that
- From the
osirisdirectory, runosiris/build-osiris-mac-osx.sh:sh build-osiris-mac-osx.sh - If there are no errors, then run
make.- There will be a lot of warnings.
- If there are no errors run
install-mac-osx.sh:sh install-mac-osx.sh.- this installs Osiris in the user's
Applicationsfolder (in the user's "Home" folder) creates a distribution file,Osiris-Mac-2.x.tar.gzin the osiris folder.
- this installs Osiris in the user's
- From the
Applicationsdirectory, runOsiris.app.