From 45e3e0299ea6454abcf3065e2e86e70f58c2f959 Mon Sep 17 00:00:00 2001
From: Petar Petrov <slackalaxy@gmail.com>
Date: Sat, 3 Aug 2019 07:11:25 +0700
Subject: academic/tophat: Updated for version 2.1.2.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/tophat/slack-desc        |  2 +-
 academic/tophat/tophat.SlackBuild | 12 +++++++-----
 academic/tophat/tophat.info       |  6 +++---
 3 files changed, 11 insertions(+), 9 deletions(-)

(limited to 'academic/tophat')

diff --git a/academic/tophat/slack-desc b/academic/tophat/slack-desc
index 72180b86b6..22fb29099f 100644
--- a/academic/tophat/slack-desc
+++ b/academic/tophat/slack-desc
@@ -14,6 +14,6 @@ tophat: high-throughput short read aligner Bowtie, and then analyzes the
 tophat: mapping results to identify splice junctions between exons.
 tophat:
 tophat: Home: http://tophat.cbcb.umd.edu/
-tophat: References: /usr/doc/tophat-2.1.1/References
+tophat: https://github.com/infphilo/tophat/
 tophat:
 tophat:
diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild
index e579ff1e9a..f32fb590f5 100644
--- a/academic/tophat/tophat.SlackBuild
+++ b/academic/tophat/tophat.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for tophat
 
-# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
+# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,13 +23,13 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=tophat
-VERSION=${VERSION:-2.1.1}
+VERSION=${VERSION:-2.1.2}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i486 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
        *) ARCH=$( uname -m ) ;;
   esac
@@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
   LIBDIRSUFFIX=""
 elif [ "$ARCH" = "i686" ]; then
   SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@@ -69,6 +69,8 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
+./autogen.sh
+
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
diff --git a/academic/tophat/tophat.info b/academic/tophat/tophat.info
index 32ecba312c..f2fc213b90 100644
--- a/academic/tophat/tophat.info
+++ b/academic/tophat/tophat.info
@@ -1,8 +1,8 @@
 PRGNAM="tophat"
-VERSION="2.1.1"
+VERSION="2.1.2"
 HOMEPAGE="http://ccb.jhu.edu/software/tophat/"
-DOWNLOAD="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz"
-MD5SUM="4b2391de46457ba6b2b7268a9da593e4"
+DOWNLOAD="https://github.com/infphilo/tophat/archive/v2.1.2/tophat-2.1.2.tar.gz"
+MD5SUM="db844fd7f53c519e716cd6222e6195b2"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
-- 
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