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academic/treerecs: Updated for version 1.2. 

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov 2020-09-16 07:31:54 +07:00 committed by Willy Sudiarto Raharjo
parent c5bfd8830e
commit eedf938615
No known key found for this signature in database
GPG Key ID: 3F617144D7238786
3 changed files with 19 additions and 21 deletions
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7
academic/treerecs/README
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@ -28,3 +28,10 @@ Bio++ use.
2) genetreeEditor: a small program which provides editing of gene names 2) genetreeEditor: a small program which provides editing of gene names
using species names and format conversion (Newick, Nhx or PhyloXML) . using species names and format conversion (Newick, Nhx or PhyloXML) .
For more information, see preprint at bioRxiv:
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations
Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau,
Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros
Stamatakis, Eric Tannier, View ORCID ProfileDavid P. Parsons
https://www.biorxiv.org/content/10.1101/782946v1

27
academic/treerecs/treerecs.SlackBuild
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@ -22,17 +22,14 @@
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# Thanks to David Parsons for clarifications about the scipt and suggestions!
PRGNAM=treerecs PRGNAM=treerecs
VERSION=${VERSION:-1.1_gitd1c1bfaf} VERSION=${VERSION:-1.2}
BUILD=${BUILD:-1} BUILD=${BUILD:-1}
TAG=${TAG:-_SBo} TAG=${TAG:-_SBo}
COMMIT=d1c1bfaf3e6f072436661c80346dee9ae54b3310 SRCNAM=Treerecs
# Depending on whether you clicked or used wget to download, the tarball
# name is different. Bleh...
WGETNAME=archive
CLICKNAME=Treerecs-master
if [ -z "$ARCH" ]; then if [ -z "$ARCH" ]; then
case "$( uname -m )" in case "$( uname -m )" in
@ -66,15 +63,9 @@ set -e
rm -rf $PKG rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT mkdir -p $TMP $PKG $OUTPUT
cd $TMP cd $TMP
rm -rf $CLICKNAME-$COMMIT rm -rf $SRCNAM-v${VERSION}
tar xvf $CWD/$SRCNAM-v${VERSION}.tar.gz
if [ -e $CWD/$WGETNAME.tar.gz ]; then cd $SRCNAM-v${VERSION}
tar xvf $CWD/$WGETNAME.tar.gz
else
tar xvf $CWD/$CLICKNAME-$COMMIT.tar.gz
fi
cd $CLICKNAME-$COMMIT
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 \
@ -87,12 +78,12 @@ cd build
cmake \ cmake \
-DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
-DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
-DCMAKE_BUILD_TYPE=MinSizeRel .. -DCMAKE_BUILD_TYPE=Release ..
make make
cd .. cd ..
# This is the program executable. Using "make install DESTDIR=$PKG" # This is the program executable. Using "make install DESTDIR=$PKG"
# works, but is simply puts the treerecs in /usr/local/bin and that's it # works, but it simply puts treerecs in /usr/local/bin and that's it
install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM
# Include the extra binaries # Include the extra binaries

6
academic/treerecs/treerecs.info
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@ -1,8 +1,8 @@
PRGNAM="treerecs" PRGNAM="treerecs"
VERSION="1.1_gitd1c1bfaf" VERSION="1.2"
HOMEPAGE="https://project.inria.fr/treerecs/" HOMEPAGE="https://project.inria.fr/treerecs/"
DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/repository/archive.tar.gz" DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz"
MD5SUM="1a378daca947481f08071b51950e021e" MD5SUM="a85d2dc0047278bfb0017c2b69824b56"
DOWNLOAD_x86_64="" DOWNLOAD_x86_64=""
MD5SUM_x86_64="" MD5SUM_x86_64=""
REQUIRES="" REQUIRES=""