00README-cygwin-binaries.txt
EPN, Wed Jul 23 10:33:55 2014

The Infernal 1.1.1 binary executable files in this directory should run
on Windows. Please read the instructions below for more information. I
have very little experience with Windows myself, but hopefully the
info below will enable you to run the binaries. Please email me if you
have questions: nawrockie@janelia.hhmi.org.

I built the Infernal 1.1.1 cygwin binaries on a virtual machine running
Windows using Cygwin. They should work for you on Windows provided
your system meets the following requirements:

- Cygwin must be installed. To install it, go to
  http://cygwin.com/setup-x86.exe. Select default options for
  everything unless you know what you're doing.

This should enable you to run the Infernal cygwin binary .exe files
when in a cygwin shell, just like you would in an other Unix/Linux
environment. See Userguide.pdf for examples (infernal.janelia.org).

If you'd like to run the binaries outside of cygwin, you can do
that too. Without a thorough understanding of what I'm actually doing,
I've been able to run the binaries inside a DOS command prompt, but
this will only work if: 

- all of Cygwin's .dll files are in your WINDOWS path. 

  These .dll files are probably in the cygwin/bin directory wherever
  you've installed cygwin. (Possibly /cygdrive/c/cygwin/bin/). You can
  either add this directory to your WINDOWS PATH environment variable,
  or copy these files to a directory that is already in your PATH. For
  example, in a cygwin shell: 'cp /cygdrive/c/cygwin/bin/*.dll
  /cygdrive/c/WINDOWS/system32/' may work (if
  /cygdrive/c/WINDOWS/system32/ is in your WINDOWS path).

Here's an example of running an infernal binary in a DOS prompt:

> "C:\Program Files\infernal-binaries\cmsearch.exe" "/cygdrive/c/Program Files/tRNA.c.cm" "/cygdrive/c/Program Files/mrum-genome.fa" > "C:\Program Files\test-cmsearch-out.txt"

Note that the path to the executable and the output file use DOS
syntax (directory slashes are "\"), while the command line arguments
to cmsearch.exe are in POSIX syntax (directory slashes are "/").

----------------------------------------
Eric Nawrocki
nawrockie@janelia.hhmi.org
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