diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/ugene/README | 14 | ||||
| -rw-r--r-- | academic/ugene/ugene.SlackBuild | 45 | ||||
| -rw-r--r-- | academic/ugene/ugene.info | 6 |
3 files changed, 43 insertions, 22 deletions
diff --git a/academic/ugene/README b/academic/ugene/README index b0a0c8064c3d2..6ef0504bd45cb 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 6ccec594dd0e8..1b758cca577aa 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 14652ce6a2e51..128db4f67cba4 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" |