From 3f66c524608d2ee461320f90653ea57db1f113da Mon Sep 17 00:00:00 2001
From: Mikhail Kviatkovskii <mikhail.kviatkovskii@pm.me>
Date: Fri, 19 Mar 2021 13:47:53 +0300
Subject: [PATCH 1/2] Building on Windows via MSYS2

---
 .github/workflows/main.yml | 37 +++++++++++++++++++++++++++++++++----
 Makefile                   |  6 ++++++
 docs/content/faq.rst       | 14 ++++++++++++++
 test/fisher/test-fisher.sh |  2 +-
 4 files changed, 54 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index caaf9902b..77dbfb161 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,17 +3,46 @@ name: CI
 on: [push, pull_request]
 
 jobs:
-  build:
+  build-linux:
 
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v1
     - name: Compile and test Bedtools
-      run: make -j8 && make test
+      run: make -j $(nproc) && make test
     - name: Compile static binary
-      run:  make -j8 static
+      run:  make -j $(nproc) static
     - uses: actions/upload-artifact@v1
       with:
-          name: bedtools.static
+          name: bedtools.static-linux
           path: bin/bedtools.static
+
+  build-windows:
+
+    runs-on: windows-latest
+
+    defaults:
+      run:
+        shell: msys2 {0}
+    steps:
+    - name: Set proper line endings in git
+      shell: powershell
+      run: git config --global core.autocrlf false
+    - uses: actions/checkout@v1
+    - uses: msys2/setup-msys2@v2
+      with:
+        msystem: MSYS
+        install: gcc make python libbz2-devel liblzma-devel zlib-devel git diffutils
+    - name: CCompile and test Bedtools
+      run: make -j $(nproc) && make test
+    - name: Compile semi-static binary
+      run: make VERBOSE=1 -j $(nproc) static
+    - name: Copy msys-2.0.dll to bin
+      run: cp /usr/bin/msys-2.0.dll bin/
+    - uses: actions/upload-artifact@v2
+      with:
+          name: bedtools.static-windows
+          path: |
+            bin/bedtools.static
+            bin/msys-2.0.dll
diff --git a/Makefile b/Makefile
index a3b3baa4a..98c81ff57 100644
--- a/Makefile
+++ b/Makefile
@@ -38,6 +38,12 @@ else
 BT_CXXFLAGS += -std=c++11
 endif
 
+# Support building on MSYS2
+UNAME := $(shell sh -c 'uname 2>/dev/null || echo Unknown')
+ifeq (MSYS_NT,$(findstring MSYS_NT,$(UNAME)))
+BT_CXXFLAGS += -D_GNU_SOURCE -D_DEFAULT_SOURCE
+endif
+
 BT_LDFLAGS =
 BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
 
diff --git a/docs/content/faq.rst b/docs/content/faq.rst
index a0298f167..91730c4dc 100644
--- a/docs/content/faq.rst
+++ b/docs/content/faq.rst
@@ -39,6 +39,20 @@ and on Fedora/Centos this would be:
     yum install zlib
     yum install zlib1g-dev
 
+--------------------------------------------------
+Is build on Windows possible?
+--------------------------------------------------
+Yes. Currently build on Windows could be done via `MSYS2 <https://www.msys2.org/>`_. You need to:
+- Install MSYS2
+- Open MSYS2 Bash shell
+- Install build dependencies via command
+.. code-block:: bash
+    pacman -S gcc make python libbz2-devel liblzma-devel zlib-devel git diffutils
+- Run ``make`` command.
+At the moment MSYS2 does not support fully static builds, so bedtools.static depends on file ``msys-2.0.dll``
+(could be found at ``C:\msys64\usr\bin\msys-2.0.dll`` if default install path is used). You need to distribute this file
+together with main executable.
+
 --------------------------------------------------
 Compiling with a specific zlib library
 --------------------------------------------------
diff --git a/test/fisher/test-fisher.sh b/test/fisher/test-fisher.sh
index d15c47d05..1a85b2b15 100644
--- a/test/fisher/test-fisher.sh
+++ b/test/fisher/test-fisher.sh
@@ -102,7 +102,7 @@ rm obs exp
 echo -e "    fisher.t5...\c"
 $BT fisher -b test.bed -a tumor.gff -g dm6.fai > exp
 DIR="${TMPDIR:-/tmp}/Users/mvandenb/src/genomic_features_bardin_lab/build/modencode/dm6/bed/"
-LONG_PATH="$DIR/AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAaS-\(phospho-S2\)_.bed"
+LONG_PATH="$DIR/AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAaS-phospho-S2_.bed"
 mkdir -p "$DIR"
 cp test.bed "$LONG_PATH"
 $BT fisher -b "$LONG_PATH" -a tumor.gff -g dm6.fai > obs

From 7f0b3a5899c972d764638787dfd7bc9b5b422d29 Mon Sep 17 00:00:00 2001
From: Mikhail Kviatkovskii <mikhail.kviatkovskii@pm.me>
Date: Fri, 19 Mar 2021 14:08:18 +0300
Subject: [PATCH 2/2] Typo fixed

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 77dbfb161..4b9d208b2 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -34,7 +34,7 @@ jobs:
       with:
         msystem: MSYS
         install: gcc make python libbz2-devel liblzma-devel zlib-devel git diffutils
-    - name: CCompile and test Bedtools
+    - name: Compile and test Bedtools
       run: make -j $(nproc) && make test
     - name: Compile semi-static binary
       run: make VERBOSE=1 -j $(nproc) static