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author Petar Petrov <slackalaxy@gmail.com>2020-09-16 07:33:44 +0700
committer Willy Sudiarto Raharjo <willysr@slackbuilds.org>2020-09-16 07:33:44 +0700
commit4980c2baef3bebb3c5b99b2a50461dc5b622d4b5 (patch)
tree87316312e934abb86ba9071b768163c7c1c88695 /academic
parenteedf938615c6ad9f06aa9b9fa04b1dc76e8f1c52 (diff)
downloadslackbuilds-4980c2baef3bebb3c5b99b2a50461dc5b622d4b5.tar.gz
slackbuilds-4980c2baef3bebb3c5b99b2a50461dc5b622d4b5.tar.xz
academic/trfind: Updated for version 4.09.1.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/trfind/trfind.SlackBuild69
-rw-r--r--academic/trfind/trfind.info10
2 files changed, 56 insertions, 23 deletions
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"