OSIRIS is 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 current…
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README.md

README.md

OSIRIS

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.

MS-Windows build

Requirements and tools

  • Most of the requirements are included with OSIRIS, except for wxwidgets. These were built with multithreading but not DLL, i.e. /MT as opposed to /MD with 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, libxslt and libiconv are 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, modified libexslt.h and changed #include <win32config.h> to #include <libxslt/win32config.h>
    • Removed all occurrences of #include <win32config.h> from all other \*.c, \*.h files and made sure that #include "libexslt/libexslt.h" is present.
    • Created VC++ projects.

Build steps

  • Download wxWidgets at http://wxwidgets.org/downloads/, either the ZIP or 7z download.
  • Download the osiris source code from https://github.com/ncbi/osiris (Version 2.3 requires an older version of wxWidgets). Or select the version from the Branch pulldown on the left side of the web page and select Download ZIP from the right side.

Build wxWidgets

  • 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%\include and %WXHOME%\lib.
  • Go to the wxWidgets build folder, then msw.
  • Select the appropriate solution .sln file for your version of Visual C++.
  • Build in Visual C++ for "Release" and Win32 and optionally for Debug and Win32. Both can coexist in the same directory structure.

Build OSIRIS

  • 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 WXHOME in the environment.
  • Make sure you are building for Release and not Debug.
  • Unpack the zip file and go to the osiris folder.
  • Open the solution file, osirisAll.sln with Visual C++ 2010 (or later).
  • Select Release and Win32 in 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 for OsirisAnalysis.exe).

Build OSIRIS .zip file for Windows - Alternative to the .msi file

  • After building OSIRIS, Run the perl script .\ZipPerl\MakeZip.pl
    • Requires cygwin, Perl, and 7zip.
    • After the above are installed, the commands, 7z and cp must be available from PATH environment variable.
  • It will set up the directory structure in .\ZipPerl\Osiris and create a .zip file.
  • If you want to create the directory structure without a zip file, then modify one line of code near the beginning of MakeZip.pl and change my $NO_ZIP_FILE = 0; to my $NO_ZIP_FILE = 1;
  • The directory structure will be in .\ZipPerl\Osiris and can be moved.

Mac OS X build

Requirements and tools

  • Mac OS X 10.9 and later build.
  • Unix command line.
  • Mac OS X Developer tools - try gcc --version to see if you have gcc available from the tools.

Build steps

  • Download wxWidgets 3.0.2 at http://wxwidgets.org/downloads/, Source for Linux, OS X, etc. (Current).
  • Download the osiris source code from https://github.com/ncbi/osiris (Version 2.3 requires an older version of wxWidgets). Or select the version from the Branch pulldown on the left side of the web page and select Download ZIP from the right side.

Build and install wxWidgets

  • 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 like wxWidgets-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 osiris directory, copy osiris/osiris/build-osx/config.sh to wxWidgets-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.
  • 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/wxRelease has four subdirectories: bin, include, lib, share
    • Set the environment variation for wxWidgets: export WXHOME=~/local/wxRelease

Build and install OSIRIS

  • From the osiris directory, run osiris/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 Applications folder (in the user's "Home" folder) creates a distribution file, Osiris-Mac-2.x.tar.gz in the osiris folder.
  • From the Applications directory, run Osiris.app.