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author Petar Petrov <slackalaxy@gmail.com>2022-09-05 16:54:07 +0100
committer Dave Woodfall <dave@slackbuilds.org>2022-09-08 08:11:03 +0100
commit81927c36c58825e15ce3bb20f7c434be2da30d93 (patch)
treea509e7af188a17321bcd3c1a7e2852328f8d8ce6
parent329edf7ded56c3a72fd3e8d0bfbb3e1bdb3f1e44 (diff)
downloadslackbuilds-81927c36c58825e15ce3bb20f7c434be2da30d93.tar.gz
slackbuilds-81927c36c58825e15ce3bb20f7c434be2da30d93.tar.xz
academic/ugene: Updated for version 44.0.
Signed-off-by: Dave Woodfall <dave@slackbuilds.org>
-rw-r--r--academic/ugene/README14
-rw-r--r--academic/ugene/ugene.SlackBuild45
-rw-r--r--academic/ugene/ugene.info6
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"