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author Petar Petrov <slackalaxy@gmail.com>2020-09-16 07:31:54 +0700
committer Willy Sudiarto Raharjo <willysr@slackbuilds.org>2020-09-16 07:31:54 +0700
commiteedf938615c6ad9f06aa9b9fa04b1dc76e8f1c52 (patch)
tree6e3ad3707250114669f53440dcf9a9c1fd3bf18a /academic
parentc5bfd8830ed6e75bb8e1507294d9a90184a18e02 (diff)
downloadslackbuilds-eedf938615c6ad9f06aa9b9fa04b1dc76e8f1c52.tar.gz
slackbuilds-eedf938615c6ad9f06aa9b9fa04b1dc76e8f1c52.tar.xz
academic/treerecs: Updated for version 1.2.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/treerecs/README7
-rw-r--r--academic/treerecs/treerecs.SlackBuild27
-rw-r--r--academic/treerecs/treerecs.info6
3 files changed, 19 insertions, 21 deletions
diff --git a/academic/treerecs/README b/academic/treerecs/README
index cd3794ca26..e338496bfb 100644
--- a/academic/treerecs/README
+++ b/academic/treerecs/README
@@ -28,3 +28,10 @@ Bio++ use.
2) genetreeEditor: a small program which provides editing of gene names
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 Gu├ęguen, 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
diff --git a/academic/treerecs/treerecs.SlackBuild b/academic/treerecs/treerecs.SlackBuild
index 4bff8e9c09..6fa09cdb0b 100644
--- a/academic/treerecs/treerecs.SlackBuild
+++ b/academic/treerecs/treerecs.SlackBuild
@@ -22,17 +22,14 @@
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# Thanks to David Parsons for clarifications about the scipt and suggestions!
+
PRGNAM=treerecs
-VERSION=${VERSION:-1.1_gitd1c1bfaf}
+VERSION=${VERSION:-1.2}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
-COMMIT=d1c1bfaf3e6f072436661c80346dee9ae54b3310
-
-# Depending on whether you clicked or used wget to download, the tarball
-# name is different. Bleh...
-WGETNAME=archive
-CLICKNAME=Treerecs-master
+SRCNAM=Treerecs
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
@@ -66,15 +63,9 @@ set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
-rm -rf $CLICKNAME-$COMMIT
-
-if [ -e $CWD/$WGETNAME.tar.gz ]; then
- tar xvf $CWD/$WGETNAME.tar.gz
-else
- tar xvf $CWD/$CLICKNAME-$COMMIT.tar.gz
-fi
-
-cd $CLICKNAME-$COMMIT
+rm -rf $SRCNAM-v${VERSION}
+tar xvf $CWD/$SRCNAM-v${VERSION}.tar.gz
+cd $SRCNAM-v${VERSION}
chown -R root:root .
find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@@ -87,12 +78,12 @@ cd build
cmake \
-DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
-DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
- -DCMAKE_BUILD_TYPE=MinSizeRel ..
+ -DCMAKE_BUILD_TYPE=Release ..
make
cd ..
# 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
# Include the extra binaries
diff --git a/academic/treerecs/treerecs.info b/academic/treerecs/treerecs.info
index 12feb2eed3..f6a81aa05b 100644
--- a/academic/treerecs/treerecs.info
+++ b/academic/treerecs/treerecs.info
@@ -1,8 +1,8 @@
PRGNAM="treerecs"
-VERSION="1.1_gitd1c1bfaf"
+VERSION="1.2"
HOMEPAGE="https://project.inria.fr/treerecs/"
-DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/repository/archive.tar.gz"
-MD5SUM="1a378daca947481f08071b51950e021e"
+DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz"
+MD5SUM="a85d2dc0047278bfb0017c2b69824b56"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""