academic/ugene: Updated for version 44.0.

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

3 files changed, 43 insertions, 22 deletions

diff --git a/academic/ugene/README b/academic/ugene/README
index b0a0c8064c..6ef0504bd4 100644
--- a/academic/ugene/README
+++ b/academic/ugene/README
@@ -38,22 +38,16 @@ program. All of them are available at SlackBuilds.org:
 - bowtie2 (A tool for aligning sequencing reads)
 - bwa (Burrows-Wheeler Aligner)
 - cap3 (CAP3: A DNA sequence assembly program)
-- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
-- cistrome-conductGO (Find the top-n highest expressed TFs)
-- cistrome-extra (Cistrome Applications Harvard extra apps)
-- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
-- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
-- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers)
 - clustalo (Clustal Omega)
 - clustalw (Multiple Sequence Alignment)
 - cufflinks (A reference-guided assembler for RNA-Seq experiments)
 - cutadapt (Trim adapters from high-throughput sequencing reads)
-- diamond (A sequence aligner for protein and translated DNA)
 - fastqc (A quality control tool for high throughput sequence data)
 - HMMER (Biosequence analysis using profile hidden Markov models)
-- kraken (Assign taxonomic labels to short DNA sequences)
-- MetaPhlAn (Metagenomic Phylogenetic Analysis)
-- ncbi-blast (BLAST: Basic Local Alignment Search Tool)
+- iqtree (Efficient and versatile phylogenomic software by ML)
+- MetaPhlAn2 (Metagenomic Phylogenetic Analysis)
+- mafft (A multiple sequence alignment program)
+- mrbayes (MrBayes: Bayesian Inference of Phylogeny)
 - ncbi-blast+ (BLAST+ Command Line Applications)
 - PhyML (Phylogenetic estimation using Maximum Likelihood)
 - samtools-legacy (Sequence Alignment/Map Tools)
diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild
index 6ccec594dd..1b758cca57 100644
--- a/academic/ugene/ugene.SlackBuild
+++ b/academic/ugene/ugene.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for ugene
 
-# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com
+# Copyright 2013-2022 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,8 +25,8 @@
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=ugene
-VERSION=${VERSION:-38.1}
-BUILD=${BUILD:-2}
+VERSION=${VERSION:-44.0}
+BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
 
@@ -84,19 +84,46 @@ find -L . \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
 # Fix libraries and man pages paths
-sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri
-sed -i "s:/share/man:/man:g" src/ugene_globals.pri
-sed -i "s:Werror=maybe-uninitialized:Wno-error=maybe-uninitialized:g
-        s:Werror=uninitialized:Wno-error=uninitialized:g" \
-  src/ugene_globals.pri
+#sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri
+#sed -i "s:/share/man:/man:g" src/ugene_globals.pri
+#sed -i "s:Werror=maybe-uninitialized:Wno-error=maybe-uninitialized:g
+#        s:Werror=uninitialized:Wno-error=uninitialized:g" \
+#  src/ugene_globals.pri
 
-qmake-qt5 $QMAKECONFIG -r \
+qmake-qt5 $QMAKECONFIG -r PREFIX=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \
 QMAKE_CFLAGS="$SLKCFLAGS" \
 QMAKE_CXXFLAGS="$SLKCFLAGS -std=c++11" \
 UGENE_EXCLUDE_LIST_ENABLED=1
 make
+
+# Apparently, this has to be done twice to generate the right installation files
+# https://github.com/ugeneunipro/ugene/issues/683#issuecomment-1046370388
+qmake-qt5 $QMAKECONFIG -r PREFIX=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \
+QMAKE_CFLAGS="$SLKCFLAGS" \
+QMAKE_CXXFLAGS="$SLKCFLAGS -std=c++11" \
+UGENE_EXCLUDE_LIST_ENABLED=1
+make
+
 make install INSTALL_ROOT=$PKG
 
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.desktop $PKG/usr/share/applications
+mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.png $PKG/usr/share/pixmaps
+
+mkdir -p $PKG/usr/man/man1
+mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.1.gz $PKG/usr/man/man1
+
+mkdir -p $PKG/usr/bin
+cd $PKG/usr/bin
+ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM .
+cd -
+
+# Do not associate with my fasta files...
+sed -i '/MimeType/d' $PKG/usr/share/applications/$PRGNAM.desktop
+
+# use just one categiry
+sed -i "s:Education;Science:Education:" $PKG/usr/share/applications/$PRGNAM.desktop
+
 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
 
diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info
index 14652ce6a2..128db4f67c 100644
--- a/academic/ugene/ugene.info
+++ b/academic/ugene/ugene.info
@@ -1,10 +1,10 @@
 PRGNAM="ugene"
-VERSION="38.1"
+VERSION="44.0"
 HOMEPAGE="http://ugene.net/"
 DOWNLOAD="UNSUPPORTED"
 MD5SUM=""
-DOWNLOAD_x86_64="https://github.com/ugeneunipro/ugene/archive/38.1/ugene-38.1.tar.gz"
-MD5SUM_x86_64="4add1b1c0216ce42e588e982a3d7147e"
+DOWNLOAD_x86_64="https://github.com/ugeneunipro/ugene/archive/44.0/ugene-44.0.tar.gz"
+MD5SUM_x86_64="17877ec046aee360a82c8d7ab7b7cf07"
 REQUIRES=""
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"