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academic/t_coffee: Updated for version 13.45.58.c355d11.

Browse source 
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Matteo Bernardini 2022-02-28 14:12:28 +01:00 committed by Willy Sudiarto Raharjo
parent 9a3af401a5
commit 137a337346
No known key found for this signature in database
GPG key ID: 3F617144D7238786
3 changed files with 17 additions and 13 deletions
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2
academic/t_coffee/README
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@ -8,6 +8,8 @@ to combine sequence information with protein structural information
3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA 3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA
secondary structures (R-Coffee). secondary structures (R-Coffee).
examples are installed in /usr/share/t_coffee/
For detailed information and citation: For detailed information and citation:
T-Coffee: A novel method for multiple sequence alignments. T-Coffee: A novel method for multiple sequence alignments.
Notredame, Higgins,Heringa,JMB,302(205-217)2000 Notredame, Higgins,Heringa,JMB,302(205-217)2000

22
academic/t_coffee/t_coffee.SlackBuild
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@ -25,13 +25,12 @@
cd $(dirname $0) ; CWD=$(pwd) cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=t_coffee PRGNAM=t_coffee
VERSION=${VERSION:-13.41.0_git28bdc39} VERSION=${VERSION:-13.45.58.c355d11}
BUILD=${BUILD:-1} BUILD=${BUILD:-1}
TAG=${TAG:-_SBo} TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz} PKGTYPE=${PKGTYPE:-tgz}
TARNAM=tcoffee TARNAM=T-COFFEE_distribution_Version
COMMIT=28bdc39911d10d8597db8513f9515fb2ed7a9158
if [ -z "$ARCH" ]; then if [ -z "$ARCH" ]; then
case "$( uname -m )" in case "$( uname -m )" in
@ -72,9 +71,9 @@ set -e
rm -rf $PKG rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT mkdir -p $TMP $PKG $OUTPUT
cd $TMP cd $TMP
rm -rf ${TARNAM}-${COMMIT} rm -rf ${TARNAM}_${VERSION}
tar xvf $CWD/${TARNAM}-${COMMIT}.tar.gz tar xvf $CWD/${TARNAM}_${VERSION}.tar.gz
cd ${TARNAM}-${COMMIT} cd ${TARNAM}_${VERSION}
chown -R root:root . chown -R root:root .
find -L . \ find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@ -83,17 +82,20 @@ find -L . \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Use our CFLAGS # Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" t_coffee/src/makefile sed -i "s|-O3 -Wno-write-strings|$SLKCFLAGS|" t_coffee_source/makefile
CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee/src CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee_source
install -D -m755 t_coffee/src/$PRGNAM $PKG/usr/bin/$PRGNAM install -D -m755 t_coffee_source/$PRGNAM $PKG/usr/bin/$PRGNAM
mkdir -p $PKG/usr/share/t_coffee
cp -a example $PKG/usr/share/t_coffee/
find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ 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 | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \ cp -a \
HOW_BUILD_WORKS.md README.md docs/*.rst \ README doc license.txt \
$PKG/usr/doc/$PRGNAM-$VERSION $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

6
academic/t_coffee/t_coffee.info
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@ -1,8 +1,8 @@
PRGNAM="t_coffee" PRGNAM="t_coffee"
VERSION="13.41.0_git28bdc39" VERSION="13.45.58.c355d11"
HOMEPAGE="http://www.tcoffee.org/" HOMEPAGE="http://www.tcoffee.org/"
DOWNLOAD="https://github.com/cbcrg/tcoffee/archive/28bdc39/tcoffee-28bdc39911d10d8597db8513f9515fb2ed7a9158.tar.gz" DOWNLOAD="https://ponce.cc/slackware/sources/repo/T-COFFEE_distribution_Version_13.45.58.c355d11.tar.gz"
MD5SUM="3392d55a2817575ce90c1c3e94e08c0b" MD5SUM="8b5d42142b531f913429dd9c2d4c8b27"
DOWNLOAD_x86_64="" DOWNLOAD_x86_64=""
MD5SUM_x86_64="" MD5SUM_x86_64=""
REQUIRES="" REQUIRES=""