diff options
Diffstat (limited to 'academic/EMBASSY/EMBASSY.SlackBuild')
| -rw-r--r-- | academic/EMBASSY/EMBASSY.SlackBuild | 306 |
1 files changed, 103 insertions, 203 deletions
diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild index 6a4d1b2794..eb67a7adcf 100644 --- a/academic/EMBASSY/EMBASSY.SlackBuild +++ b/academic/EMBASSY/EMBASSY.SlackBuild @@ -1,17 +1,31 @@ #!/bin/sh # Slackware build script for EMBASSY -# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and -# hereby submitted to the public domain -# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING -# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ -# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. - -PRGNAM=EMBASSY -VERSION=${VERSION:-6.4.0} # Keep this the same as the version of EMBOSS. +# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE + +PRGNAM=EMBASSY +VERSION=${VERSION:-6.5.7} # Keep this the same version as EMBOSS BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -40,6 +54,26 @@ else LIBDIRSUFFIX="" fi +# EMBASSY components and their versions +CBSTOOLS=CBSTOOLS-1.0.0.650 +CLUSTALOMEGA=CLUSTALOMEGA-0.2.0.650 +DOMAINATRIX=DOMAINATRIX-0.1.650 +DOMALIGN=DOMALIGN-0.1.650 +DOMSEARCH=DOMSEARCH-0.1.650 +EMNU=EMNU-1.05.650 +ESIM4=ESIM4-1.0.0.650 +HMMER=HMMER-2.3.2.650 +IPRSCAN=IPRSCAN-4.3.1.650 +MEME=MEME-4.7.650 +MSE=MSE-3.0.0.650 +MYEMBOSS=MYEMBOSS-6.5.1 +MYEMBOSSDEMO=MYEMBOSSDEMO-6.5.0 +PHYLIPNEW=PHYLIPNEW-3.69.650 +SIGNATURE=SIGNATURE-0.1.650 +STRUCTURE=STRUCTURE-0.1.650 +TOPO=TOPO-2.0.650 +VIENNA=VIENNA-1.7.2.650 + set -e rm -rf $PKG @@ -47,11 +81,28 @@ mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION mkdir $TMP/$PRGNAM-$VERSION - -# Build CBSTOOLS cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/CBSTOOLS-*.tar.gz -cd CBSTOOLS-* + +# Extract the components +tar xvf $CWD/$CBSTOOLS.tar.gz +tar xvf $CWD/$CLUSTALOMEGA.tar.gz +tar xvf $CWD/$DOMAINATRIX.tar.gz +tar xvf $CWD/$DOMALIGN.tar.gz +tar xvf $CWD/$DOMSEARCH.tar.gz +tar xvf $CWD/$EMNU.tar.gz +tar xvf $CWD/$ESIM4.tar.gz +tar xvf $CWD/$HMMER.tar.gz +tar xvf $CWD/$IPRSCAN.tar.gz +tar xvf $CWD/$MEME.tar.gz +tar xvf $CWD/$MSE.tar.gz +tar xvf $CWD/$MYEMBOSS.tar.gz +tar xvf $CWD/$MYEMBOSSDEMO.tar.gz +tar xvf $CWD/$PHYLIPNEW.tar.gz +tar xvf $CWD/$SIGNATURE.tar.gz +tar xvf $CWD/$STRUCTURE.tar.gz +tar xvf $CWD/$TOPO.tar.gz +tar xvf $CWD/$VIENNA.tar.gz + chown -R root:root . find . \ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -59,6 +110,8 @@ find . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +# Build CBSTOOLS +cd $TMP/$PRGNAM-$VERSION/$CBSTOOLS CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -68,21 +121,12 @@ CXXFLAGS="$SLKCFLAGS" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ - --build=$ARCH-slackware-linux + --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build CLUSTALOMEGA -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/CLUSTALOMEGA-*.tar.gz -cd CLUSTALOMEGA-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$CLUSTALOMEGA CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -94,19 +138,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build DOMAINATRIX -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/DOMAINATRIX-*.tar.gz -cd DOMAINATRIX-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$DOMAINATRIX CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -118,19 +153,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build DOMALIGN -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/DOMALIGN-*.tar.gz -cd DOMALIGN-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$DOMALIGN CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -142,19 +168,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build DOMSEARCH -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/DOMSEARCH-*.tar.gz -cd DOMSEARCH-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$DOMSEARCH CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -166,19 +183,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build EMNU -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/EMNU-*.tar.gz -cd EMNU-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$EMNU CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -190,19 +198,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build ESIM4 -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/ESIM4-*.tar.gz -cd ESIM4-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$ESIM4 CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -214,19 +213,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build HMMER -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/HMMER-*.tar.gz -cd HMMER-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$HMMER CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -238,19 +228,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build IPRSCAN -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/IPRSCAN-*.tar.gz -cd IPRSCAN-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$IPRSCAN CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -262,19 +243,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build MEME -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/MEME-*.tar.gz -cd MEME-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$MEME CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -286,19 +258,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/MEME \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build MSE -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/MSE-*.tar.gz -cd MSE-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$MSE CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -310,19 +273,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/MSE \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build MYEMBOSS -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/MYEMBOSS-*.tar.gz -cd MYEMBOSS-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$MYEMBOSS CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -334,19 +288,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build MYEMBOSSDEMO -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/MYEMBOSSDEMO-*.tar.gz -cd MYEMBOSSDEMO-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$MYEMBOSSDEMO CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -358,19 +303,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build PHYLIPNEW -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/PHYLIPNEW-*.tar.gz -cd PHYLIPNEW-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$PHYLIPNEW CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -382,19 +318,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build SIGNATURE -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/SIGNATURE-*.tar.gz -cd SIGNATURE-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$SIGNATURE CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -406,19 +333,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build STRUCTURE -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/STRUCTURE-*.tar.gz -cd STRUCTURE-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$STRUCTURE CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -430,19 +348,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG # Build TOPO -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/TOPO-*.tar.gz -cd TOPO-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$TOPO CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -454,19 +363,10 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install - +make install DESTDIR=$PKG + # Build VIENNA -cd $TMP/$PRGNAM-$VERSION -tar xvf $CWD/VIENNA-*.tar.gz -cd VIENNA-* -chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - +cd $TMP/$PRGNAM-$VERSION/$VIENNA CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -478,7 +378,7 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install +make install DESTDIR=$PKG 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 |