From 4980c2baef3bebb3c5b99b2a50461dc5b622d4b5 Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Wed, 16 Sep 2020 07:33:44 +0700
Subject: academic/trfind: Updated for version 4.09.1.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/trfind/trfind.SlackBuild | 69 +++++++++++++++++++++++++++++----------
 academic/trfind/trfind.info       | 10 +++---
 2 files changed, 56 insertions(+), 23 deletions(-)

(limited to 'academic')

diff --git a/academic/trfind/trfind.SlackBuild b/academic/trfind/trfind.SlackBuild
index 76783294e3..22702f68c8 100644
--- a/academic/trfind/trfind.SlackBuild
+++ b/academic/trfind/trfind.SlackBuild
@@ -23,16 +23,15 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=trfind
-VERSION=${VERSION:-4.09}
-BUILD=${BUILD:-2}
+VERSION=${VERSION:-4.09.1}
+BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
-SRCNAM=trf
-BINVER=409
+SRCNAM=TRF
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i386 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
        *) ARCH=$( uname -m ) ;;
   esac
@@ -43,30 +42,64 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-set -e
-
-if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
-  printf "\n\n$ARCH is not supported... \n"
-  exit 1
-fi
-
-# Determine binary architecture
-if [ "$ARCH" = "x86_64" ]; then
-  BINARCH="linux64"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
 else
-  BINARCH="linux32"
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
 fi
 
+set -e
+
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+CFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+
+make
+
+# "make install" works, but it is simpler this way
+install -D -m755 src/trf $PKG/usr/bin/trf
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
-install -D -m755 $CWD/${SRCNAM}${BINVER}.${BINARCH} $PKG/usr/bin/$SRCNAM
+# Include FASTA examples, but let's compress the file first
+mkdir -p $PKG/usr/share/$PRGNAM
+gzip test_seqs.fasta
+cp test_seqs.fasta.gz $PKG/usr/share/$PRGNAM
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  README.md COPYING INSTALL history.txt \
+  $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
-cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE
 
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
diff --git a/academic/trfind/trfind.info b/academic/trfind/trfind.info
index 2dfb07986d..adaf4da150 100644
--- a/academic/trfind/trfind.info
+++ b/academic/trfind/trfind.info
@@ -1,10 +1,10 @@
 PRGNAM="trfind"
-VERSION="4.09"
+VERSION="4.09.1"
 HOMEPAGE="https://tandem.bu.edu/trf/trf.html"
-DOWNLOAD="http://tandem.bu.edu/trf/downloads/trf409.linux32"
-MD5SUM="285478f16f417d6e9c9700f556373e43"
-DOWNLOAD_x86_64="http://tandem.bu.edu/trf/downloads/trf409.linux64"
-MD5SUM_x86_64="0c594fe666e0332db1df9d160d7fabc8"
+DOWNLOAD="https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1/TRF-4.09.1.tar.gz"
+MD5SUM="8569300f69776b65e22ad12caa682ab8"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
 REQUIRES=""
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"
-- 
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