@*~RSC_HELP_PCKG_NO_COMPILER In Strap, bioinformatics programs are installed from source code using the C, C++ or Fortran compilers and make. What happens without compilers? Ready-to-use executables for ClustalW and TM-align are available for Windows, Mac and Linux systems with x86 and AMD64 architecture. They will be downloaded to HTMLDOC_FILE:DIR_BIN. After download they will be tested because of the inherent risk of binary incompatibility. In case they fail to run, they are deactivated by appending the suffix SFX_BINARY_FAILED to the file name. Without TM-align, a Java library for 3D-superposition will be used as a fall back. *@ @*~RSC_HELP_PCKG_WIN Four environments for software installation from source code are supported: MINGW, Rtools, MSYS2 and Cygwin. They are recognized if installed at their standard location (X:\ stands for any drive letter):
HTMLDOC_TEXT:SYSP_MSG_PATH_FOR_MINGW_CYGWIN
Strap will scan these locations. The following have been identified:
HTMLDOC_TEXT:SYSP_MSG_INSTALLED_MINGW_CYGWIN.
Furthermore LaTeX is required for PDF generation. The recommended LaTeX distribution for Windows is MiKTeX.

Options:
  1. Install none. HTMLDOC_TEXT_RSC:RSC_HELP_PCKG_NO_COMPILER Without LaTeX there will be no PDF export of the alignment.
  2. Install MINGW (Size on HD 500 MB) and MiKTeX (Size on HD 530 MB) (Most Recommended).
  3. Install MSYS2 (Size on HD 1.7 GB) and MiKTeX (Size on HD 500 MB) (Recommended).
  4. Install Cygwin from https://cygwin.org (1GB on HD). in the Cygwin setup, activate the following:
          gcc g++ fortran make
          pdflatex poppler ghostscript imagemagick pdf2svg pdf2svg pdfcrop
          odt2txt catdoc
          texlive-collection-latex
          texlive-collection-basic
          texlive-collection-extra
        
  5. Use existing C:\Rtools\ installation which comes with the statistics package R. Add MiKTeX (Size on HD 530 MB) and PERL.

Comparison of MINGW, MSYS2 and Cygwin

Which one to go for - this depends on whether and how it will be used otherwise and how much HD space is available.

Cygwin is the most comprehensive and most compatible UNIX like environment. Almost all bioinformatics programs used in Strap can be compiled in Cygwin. The disadvantage is that compiled programs often only run in the Cygwin environment which causes a slight delay when programs are launched by Strap.

Conversely, compilation with MINGW and the derivatives Rtools and MSYS2 yields executable programs that run natively under Windows. While all tools can be easily installed by their setup program, MSYS2 also reqires an additional installation step: The MSYS2 console needs to be opened to enter pacman commands as described above. The disadvantage is that with MINGW, Rtools and MSYS2, a small number of alignment back-ends cannot be compiled. *@