Initial version for CONTRAfold package

4 files changed, 72 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..8232313b0503
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,18 @@
+pkgbase = contrafold
+	pkgdesc = CONditional TRAining for RNA Secondary Structure Prediction
+	pkgver = 2.02
+	pkgrel = 1
+	url = http://contra.stanford.edu/contrafold/
+	arch = i686
+	arch = x86_64
+	license = BSD
+	makedepends = gcc>=4.1.3
+	source = http://contra.stanford.edu/contrafold/contrafold_v2_02.tar.gz
+	source = LBFGS.patch
+	source = Utilities.patch
+	md5sums = cea66c63df835fe7f790c7f49ce83ef3
+	md5sums = 7f5cc03bb145d7f4ff8e18ede22bbdd7
+	md5sums = 1edad72c52d336a0fa17862371dd60d0
+
+pkgname = contrafold
+
diff --git a/LBFGS.patch b/LBFGS.patch
new file mode 100644
index 000000000000..cef5d4070328
--- /dev/null
+++ b/LBFGS.patch
@@ -0,0 +1,11 @@
+--- LBFGS.ipp.orig	2016-04-15 10:46:11.527249307 +0200
++++ LBFGS.ipp	2016-04-15 10:46:21.377843414 +0200
+@@ -107,7 +107,7 @@
+ 
+         // perform line search, update f, and take step
+ 
+-        Real step = DoLineSearch(x[k%2], f[k%2], g[k%2], d,
++        Real step = this->DoLineSearch(x[k%2], f[k%2], g[k%2], d,
+                                  x[(k+1)%2], f[(k+1)%2], g[(k+1)%2],
+                                  Real(0), std::min(Real(10), MAX_STEP_NORM / std::max(Real(1), Norm(d))));
+         
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..9043da72168b
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,33 @@
+# Maintainer: Tomasz Zok <tomasz.zok [at] gmail.com>
+pkgname=contrafold
+pkgver=2.02
+pkgrel=1
+pkgdesc="CONditional TRAining for RNA Secondary Structure Prediction"
+arch=('i686' 'x86_64')
+url="http://contra.stanford.edu/contrafold/"
+license=('BSD')
+makedepends=('gcc>=4.1.3')
+source=("http://contra.stanford.edu/contrafold/${pkgname}_v${pkgver/./_}.tar.gz"
+        "LBFGS.patch"
+        "Utilities.patch")
+md5sums=('cea66c63df835fe7f790c7f49ce83ef3'
+         '7f5cc03bb145d7f4ff8e18ede22bbdd7'
+         '1edad72c52d336a0fa17862371dd60d0')
+
+prepare() {
+	cd "$pkgname/src"
+	patch -p0 -i "$srcdir/LBFGS.patch"
+	patch -p0 -i "$srcdir/Utilities.patch"
+}
+
+build() {
+	cd "$pkgname/src"
+	make clean
+    make
+}
+
+package() {
+	cd "$pkgname/src"
+    install -d "$pkgdir/usr/bin/"
+    install contrafold "$pkgdir/usr/bin/"
+}
diff --git a/Utilities.patch b/Utilities.patch
new file mode 100644
index 000000000000..adde758a2356
--- /dev/null
+++ b/Utilities.patch
@@ -0,0 +1,10 @@
+--- Utilities.hpp.orig	2016-04-15 10:47:13.031387314 +0200
++++ Utilities.hpp	2016-04-15 10:47:26.417272828 +0200
+@@ -24,6 +24,7 @@
+ #include <string>
+ #include <sys/time.h>
+ #include <vector>
++#include <limits.h>
+ 
+ typedef unsigned char BYTE;
+ const char DIR_SEPARATOR_CHAR = '/';