Ported in the homebrew-marauder for a hacky update/import system.

	TODO: Maybe add a license & fix up messy code.

7 files changed, 61 insertions, 0 deletions

diff --git a/homebrew/abyss/.beer b/homebrew/abyss/.beer
new file mode 100644
index 000000000..34695336b
--- /dev/null
+++ b/homebrew/abyss/.beer
@@ -0,0 +1,53 @@
+{
+    "name": "Abyss",
+    "description": "Genome sequence assembler for short reads",
+    "url": "https://github.com/bcgsc/abyss/releases/download/2.1.5/abyss-2.1.5.tar.gz",
+    "mirror": null,
+    "homepage": "http://www.bcgsc.ca/platform/bioinfo/software/abyss",
+    "depends": [
+        {
+            "depend": "autoconf",
+            "build-depend": true
+        },
+        {
+            "depend": "automake",
+            "build-depend": true
+        },
+        {
+            "depend": "multimarkdown",
+            "build-depend": true
+        },
+        {
+            "depend": "boost",
+            "build-depend": true
+        },
+        {
+            "depend": "google-sparsehash",
+            "build-depend": true
+        },
+        {
+            "depend": "gcc",
+            "build-depend": false
+        },
+        {
+            "depend": "open-mpi",
+            "build-depend": false
+        }
+    ],
+    "resource": [],
+    "conflicts": [],
+    "patches": [],
+    "install": [
+        "system \"./autogen.sh\" if build.head?",
+        "system \"./configure\", \"--enable-maxk=128\",",
+        "\"--prefix=#{prefix}\",",
+        "\"--with-boost=#{Formula[\"boost\"].include}\",",
+        "\"--with-mpi=#{Formula[\"open-mpi\"].prefix}\",",
+        "\"--with-sparsehash=#{Formula[\"google-sparsehash\"].prefix}\",",
+        "\"--disable-dependency-tracking\",",
+        "\"--disable-silent-rules\"",
+        "system \"make\", \"install\""
+    ],
+    "version": "2.1.5",
+    "file": "abyss.rb"
+}
\ No newline at end of file
diff --git a/homebrew/abyss/.make.sh-auto b/homebrew/abyss/.make.sh-auto
new file mode 100644
index 000000000..1ed8be645
--- /dev/null
+++ b/homebrew/abyss/.make.sh-auto
@@ -0,0 +1,3 @@
+pkg:setup
+pkg:configure --enable-maxk=128 --with-boost=#{Formula[boost"].include}" --with-mpi=#{Formula[open-mpi"].prefix}" --with-sparsehash=#{Formula[google-sparsehash"].prefix}" --disable-dependency-tracking --disable-silent-rules
+make DESTDIR=${PKG_DEST} install
diff --git a/homebrew/abyss/_metadata/description b/homebrew/abyss/_metadata/description
new file mode 100644
index 000000000..43a17bdd8
--- /dev/null
+++ b/homebrew/abyss/_metadata/description
@@ -0,0 +1 @@
+Genome sequence assembler for short reads
diff --git a/homebrew/abyss/_metadata/homepage b/homebrew/abyss/_metadata/homepage
new file mode 100644
index 000000000..d37a23e10
--- /dev/null
+++ b/homebrew/abyss/_metadata/homepage
@@ -0,0 +1 @@
+http://www.bcgsc.ca/platform/bioinfo/software/abyss
diff --git a/homebrew/abyss/_metadata/name b/homebrew/abyss/_metadata/name
new file mode 100644
index 000000000..c9bd77679
--- /dev/null
+++ b/homebrew/abyss/_metadata/name
@@ -0,0 +1 @@
+Abyss
diff --git a/homebrew/abyss/_metadata/version b/homebrew/abyss/_metadata/version
new file mode 100644
index 000000000..cd57a8b95
--- /dev/null
+++ b/homebrew/abyss/_metadata/version
@@ -0,0 +1 @@
+2.1.5
diff --git a/homebrew/abyss/download.sh b/homebrew/abyss/download.sh
new file mode 100755
index 000000000..cbf7155b2
--- /dev/null
+++ b/homebrew/abyss/download.sh
@@ -0,0 +1 @@
+wget https://github.com/bcgsc/abyss/releases/download/2.1.5/abyss-2.1.5.tar.gz
\ No newline at end of file