Mingw build

.gitignore

@@ -1,4 +1,3 @@
-configure
 config.log
 config.status
 Makefile
@@ -7,6 +6,8 @@ easel
 *.o
 *.dSYM
 *.stamp
+*.exe
+!binaries/*.exe
 src/*_example
 src/*_example?
 src/*_utest
@@ -47,3 +48,4 @@ src/makehmmerdb
 src/nhmmer
 src/nhmmscan
 src/phmmer
+mman-win32/

README.md

@@ -1,3 +1,129 @@
+# Port of HMMER to Windows using MinGW
+
+This project is a port of HMMER source code to the [MInGW](https://www.mingw-w64.org) compiler.  
+
+With the exception of `hmmpgmd` and `hmmpgmd_shard` the Windows native executables pass all tests.
+
+If prefer not to do your own build the resulting executables are in the [binaries](/binaries) directory.
+
+The source code in this project was created from [hmmer](https://github.com/jones-gareth/hmmer/tree/mingw-build)
+and [easel](https://github.com/jones-gareth/easel/tree/mingw-build) forks of the develop branches 
+of [HMMER](https://github.com/EddyRivasLab/hmmer/tree/develop).
+
+## Build Recipe
+
+The following recipe describes how to build native executables for windows using 
+[MSYS2](https://www.msys2.org/) and [MInGW](https://www.mingw-w64.org/). At the time
+ of writing the compiler was `gcc version 11.2.0 (Rev1, Built by MSYS2 project)`
+
+**Prerequisites**
+
+Prior to building install MSYS2, For example use [chocolately](https://chocolatey.org/) 
+(`choco.exe install msys2`), or an
+[installer](https://repo.msys2.org/distrib/x86_64/)
+
+In the MSYS2 shell install these packages (picking all groups)
+
+```console
+pacman -S base-devel gcc vim cmake 
+pacman -S mingw-w64-x86_64-toolchain
+pacman -S diffutils
+```
+
+There is no mman library for windows, but a wrapper is available for MinGW.  
+Download it from [github](https://github.com/alitrack/mman-win32) and build 
+in MSYS2 (here installing it to c:\local).
+
+```console
+./configure --prefix=c:/local
+mingw32-make.exe 
+mingw32-make.exe install
+```
+
+**Download code**
+
+```console
+git clone https://github.com/jones-gareth/hmmer
+cd hmmer
+git clone https://github.com/jones-gareth/easel
+```
+
+**Configure HMMER**
+
+If `configure` is not present it will need to be generated on a LINUX system using `autoconf`.
+
+Run configure (here installing to c:\local and looking for mman header files and library in c:\local):
+
+```console
+CPPFLAGS="-Ic:/local/include" LDFLAGS=" -static -Lc:/local/lib" CFLAGS="-g -O0" ./configure --prefix=c:/local
+```
+Check that configure has picked up the mman library.
+
+```console
+HMMER configuration:
+   compiler:             gcc -g -O0   -pthread
+   host:                 x86_64-w64-mingw32
+   linker:                -static -Lc:/local/lib
+   libraries:            -lmman   -lpthread
+   DP implementation:    sse
+```
+
+**Make, test and install**  
+
+```console
+mingw32-make.exe clean
+mingw32-make.exe dev           # build everything- there should be no warnings
+rm -rf src/impl                
+cp -r src/impl_sse src/impl    # No symlinks on windows, so this needs to be copied
+mingw32-make.exe check         # Run the tests. 2 will fail
+mingw32-make.exe install       # install if you're happy with test results
+```
+
+### Porting notes
+
+The presence of carriage returns (`\r`) in `config.sub` or `config.guess` will cause `autoconf` to fail.
+Git operations may result in the insertion of `\r` depending on the `core.autocrlf` setting.
+
+Windows (and MinGW) do not support POSIX signals or sockets.  Lack of socket support
+mean that the  client server daemon 
+commands `hmmpgmd` and `hmmpgmd_shard` do not function (the executables are compiled, but they
+won't work.)
+
+Use of shell commands in C system calls is not properly supported.  For example, code like 
+
+```C
+popen("cat esltmpfile 2>/dev/null");
+system("gzip -c eslfile 2>/dev/null > eslfile.gz");
+```
+
+Will compile but not generally run (at least not in any portable fashion).
+I  disabled unit tests that use this type of code.
+
+1. Case 5 in esl_buffer_utest::main
+2. esl_buffer_utest::utestOpenPipe
+3. The gzip output case in esl_buffer_utest::utestSetOffset
+4. esl_buffer_utest::utest_halfnewline (requires signals)
+
+The temporary files created by `esl_tmpfile` will persist on the filesystem in TEMP.
+In Windows it is not possible to delete a file that is in use.
+
+### Failed tests
+
+All tests except `hmmpgmd_ga` and `hmmpgmd_shard_ga` should pass.
+Since the `hmmpgmd` and `hmmpgmd_shard` commands are broken that is expected.
+
+```console
+    exercise  297 [           hmmpgmd_ga] ...     FAILED [command failed]
+    exercise  299 [     hmmpgmd_shard_ga] ...     FAILED [command failed]
+
+2 of 307 exercises at level <= 2 FAILED.
+```
+
+The tests use the perl and python executables installed in the MSYS2 shell.
+
+Test code at a level > 2 has not been ported and may not run correctly (because of windows text mode,
+the test scripts frequently need changes even when the commands function correctly).
+
 ## HMMER - biological sequence analysis using profile HMMs
 
 [![](https://travis-ci.org/EddyRivasLab/hmmer.svg?branch=develop)](https://travis-ci.org/EddyRivasLab/hmmer)