bamtools 1.0.2

Closes #12861.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>

1 files changed, 70 insertions, 0 deletions

diff --git a/Library/Formula/bamtools.rb b/Library/Formula/bamtools.rb
new file mode 100644
index 000000000..7f8aea29c
--- /dev/null
+++ b/Library/Formula/bamtools.rb
@@ -0,0 +1,70 @@
+require 'formula'
+
+class Bamtools < Formula
+  homepage 'https://github.com/pezmaster31/bamtools'
+  url 'https://github.com/downloads/pezmaster31/bamtools/bamtools-1.0.2.tar.gz'
+  sha1 '70d4a1f8d7da73dd381b609b618ed19b6184366e'
+
+  head 'https://github.com/pezmaster31/bamtools.git'
+
+  depends_on 'cmake' => :build
+
+  # Install libbamtools in /usr/local/lib.
+  # Link statically with libbamtools-util and libjsoncpp, since
+  # they're not installed by default. Sent upstream:
+  # https://github.com/pezmaster31/bamtools/pull/55
+  def patches
+     DATA
+  end
+
+  def install
+    mkdir 'default' do
+      system "cmake", "..", *std_cmake_args
+      system "make install"
+    end
+  end
+
+  def test
+    system "#{bin}/bamtools", "--version"
+  end
+end
+
+__END__
+diff -ur bamtools-1.0.2.orig/src/api/CMakeLists.txt bamtools-1.0.2/src/api/CMakeLists.txt
+--- bamtools-1.0.2.orig/src/api/CMakeLists.txt	2011-09-09 18:59:44.000000000 -0700
++++ bamtools-1.0.2/src/api/CMakeLists.txt	2012-06-15 10:46:18.000000000 -0700
+@@ -54,8 +54,8 @@
+ target_link_libraries( BamTools-static z )
+
+ # set library install destinations
+-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
++install( TARGETS BamTools LIBRARY DESTINATION "lib" RUNTIME DESTINATION "bin")
++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib")
+
+ # export API headers
+ include(../ExportHeader.cmake)
+diff -ur bamtools-1.0.2.orig/src/third_party/jsoncpp/CMakeLists.txt bamtools-1.0.2/src/third_party/jsoncpp/CMakeLists.txt
+--- bamtools-1.0.2.orig/src/third_party/jsoncpp/CMakeLists.txt	2012-06-15 10:39:40.000000000 -0700
++++ bamtools-1.0.2/src/third_party/jsoncpp/CMakeLists.txt	2012-06-15 10:41:49.000000000 -0700
+@@ -10,7 +10,7 @@
+ add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
+
+ # create jsoncpp library
+-add_library ( jsoncpp SHARED
++add_library ( jsoncpp STATIC
+               json_reader.cpp
+               json_value.cpp
+               json_writer.cpp
+diff -ur bamtools-1.0.2.orig/src/utils/CMakeLists.txt bamtools-1.0.2/src/utils/CMakeLists.txt
+--- bamtools-1.0.2.orig/src/utils/CMakeLists.txt	2012-06-15 10:39:40.000000000 -0700
++++ bamtools-1.0.2/src/utils/CMakeLists.txt	2012-06-15 10:41:34.000000000 -0700
+@@ -13,7 +13,7 @@
+ add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
+
+ # create BamTools utils library
+-add_library ( BamTools-utils SHARED
++add_library ( BamTools-utils STATIC
+               bamtools_fasta.cpp
+               bamtools_options.cpp
+               bamtools_pileup_engine.cpp