diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/treebest-ensembl/README | 29 | ||||
| -rw-r--r-- | academic/treebest-ensembl/doinst.sh | 3 | ||||
| -rw-r--r-- | academic/treebest-ensembl/slack-desc | 19 | ||||
| -rw-r--r-- | academic/treebest-ensembl/treebest-ensembl.SlackBuild | 112 | ||||
| -rw-r--r-- | academic/treebest-ensembl/treebest-ensembl.info | 10 | ||||
| -rw-r--r-- | academic/treebest-ensembl/treebest.desktop | 8 | ||||
| -rw-r--r-- | academic/treebest-ensembl/treebest.png | bin | 0 -> 10124 bytes |
7 files changed, 181 insertions, 0 deletions
diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README new file mode 100644 index 0000000000..b6639d304d --- /dev/null +++ b/academic/treebest-ensembl/README @@ -0,0 +1,29 @@ +TreeBeST: Tree Building guided by Species Tree +(Ensembl Compara modifications) + +TreeBeST, which stands for (gene) Tree Building guided by Species Tree, +is a versatile program that builds, manipulates and displays +phylogenetic trees. It is particularly designed for building gene trees +with a known species tree and is highly efficient and accurate. + +TreeBeST is previously known as NJTREE. It has been largely used in the +TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting +group. + +This is the Ensembl Compara modifications version. The main new features +are: + +1) -s option in treebest sdi, to allow a user-defined species tree. + T node-tag in the NHX output: a bit-field listing the input trees +2) that support the node. +3) -I option in treebest nj, to carry on the T tags from the input tree +4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK +5) -X option in treebest best, to give a higher weight to the likelihood + that comes from the reconciliation with the species tree (default 1) +6) -I option in treebest best, to start from the input tree instead of + building one +7) Species-intersection scores are now also reported as floating-point + values under the DCS node-tag. The value is between 0 and 1, and + displayed with 4 decimals. + +The script builds both the command line and GUI versions of treebest. diff --git a/academic/treebest-ensembl/doinst.sh b/academic/treebest-ensembl/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/treebest-ensembl/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/treebest-ensembl/slack-desc b/academic/treebest-ensembl/slack-desc new file mode 100644 index 0000000000..88564708b1 --- /dev/null +++ b/academic/treebest-ensembl/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +treebest-ensembl: treebest-ensembl (Tree Building guidEd by Species Tree) +treebest-ensembl: +treebest-ensembl: TreeBeST, which stands for (gene) Tree Building guided by Species +treebest-ensembl: Tree, is a versatile program that builds, manipulates and displays +treebest-ensembl: phylogenetic trees. It is particularly designed for building gene +treebest-ensembl: trees with a known species tree and is highly efficient and accurate. +treebest-ensembl: +treebest-ensembl: This is TreeBeST with Ensembl Compara modifications. +treebest-ensembl: +treebest-ensembl: http://treesoft.sourceforge.net/ +treebest-ensembl: https://github.com/Ensembl/treebest diff --git a/academic/treebest-ensembl/treebest-ensembl.SlackBuild b/academic/treebest-ensembl/treebest-ensembl.SlackBuild new file mode 100644 index 0000000000..b3a8844539 --- /dev/null +++ b/academic/treebest-ensembl/treebest-ensembl.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/sh + +# Slackware build script for treebest + +# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=treebest-ensembl +VERSION=${VERSION:-1.9.2_git347fa82} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=treebest +COMMIT=347fa82a0ce1c169849053fdc9ff7d19d221f290 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$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 + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$COMMIT +tar xvf $CWD/$SRCNAM-$COMMIT.tar.gz +cd $SRCNAM-$COMMIT +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 {} \; + +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile + +# Make the CLI treebest and the FLTK GUI +CFLAGS="$SLKCFLAGS" \ +make + +CFLAGS="$SLKCFLAGS" \ +make fltreebest + +install -D -m755 treebest $PKG/usr/bin/treebest +install -D -m755 fltreebest $PKG/usr/bin/fltreebest +install -D -m755 make_ng86 $PKG/usr/bin/make_ng86 + +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 + +# Pack some exmples and scripts +mkdir -p $PKG/usr/share/$PRGNAM +cp -a examples scripts $PKG/usr/share/$PRGNAM + +# Use our icon +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$SRCNAM.desktop $PKG/usr/share/applications +cp $CWD/$SRCNAM.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ACKNOWLEDGEMENTS AUTHORS ChangeLog COPYING FUTURES INSTALL NEWS README.md treebest.texi \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/treebest-ensembl/treebest-ensembl.info b/academic/treebest-ensembl/treebest-ensembl.info new file mode 100644 index 0000000000..8e97295a93 --- /dev/null +++ b/academic/treebest-ensembl/treebest-ensembl.info @@ -0,0 +1,10 @@ +PRGNAM="treebest-ensembl" +VERSION="1.9.2_git347fa82" +HOMEPAGE="https://github.com/Ensembl/treebest/" +DOWNLOAD="https://github.com/Ensembl/treebest/archive/347fa82/treebest-347fa82a0ce1c169849053fdc9ff7d19d221f290.tar.gz" +MD5SUM="619622cadea6da5d9c74defa761cfdda" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="fltk" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/treebest-ensembl/treebest.desktop b/academic/treebest-ensembl/treebest.desktop new file mode 100644 index 0000000000..cff35dd7b0 --- /dev/null +++ b/academic/treebest-ensembl/treebest.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=Tree Building guidEd by Species Tree +Exec=fltreebest +Icon=treebest +Name=FLTreeBeST +StartupNotify=false +Type=Application diff --git a/academic/treebest-ensembl/treebest.png b/academic/treebest-ensembl/treebest.png Binary files differnew file mode 100644 index 0000000000..e9b30dc447 --- /dev/null +++ b/academic/treebest-ensembl/treebest.png |
