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| -rw-r--r-- | academic/EMBASSY/CONTENTS | 94 | ||||
| -rw-r--r-- | academic/EMBASSY/EMBASSY.SlackBuild | 494 | ||||
| -rw-r--r-- | academic/EMBASSY/EMBASSY.info | 44 | ||||
| -rw-r--r-- | academic/EMBASSY/README | 23 | ||||
| -rw-r--r-- | academic/EMBASSY/slack-desc | 19 |
5 files changed, 674 insertions, 0 deletions
diff --git a/academic/EMBASSY/CONTENTS b/academic/EMBASSY/CONTENTS new file mode 100644 index 0000000000000..d739dcfb711ec --- /dev/null +++ b/academic/EMBASSY/CONTENTS @@ -0,0 +1,94 @@ +The EMBASSY package includes the following: +------------------------------------------- + +DOMAINATRIX Previous distributions of the protein domain programs from +Jon Ison's group were in a single EMBASSY package. This is now split +into 5 packages according to function. + +Application details and documentation for DOMAINATRIX + +DOMAINATRIX is available as a Beta release 0.1.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMAINATRIX-0.1.0.tar.gz + +Application details and documentation for DOMALIGN + +DOMALIGN is available as a Beta release 0.1.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMALIGN-0.1.0.tar.gz + +Application details and documentation for DOMSEARCH + +DOMSEARCH is available as a Beta release 0.1.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMSEARCH-0.1.0.tar.gz + +Application details and documentation for SIGNATURE + +SIGNATURE is available as a Beta release 0.1.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file SIGNATURE-0.1.0.tar.gz + +Application details and documentation for STRUCTURE + +STRUCTURE is available as a Beta release 0.1.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file STRUCTURE-0.1.0.tar.gz EMNU +(EMBOSS Menu is Not UNIX) Application details and documentation for EMNU + +EMNU is available as release 1.05 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file EMNU-1.05.tar.gz ESIM4 +(EMBOSS version of SIM4) Application details and documentation for ESIM4 + +ESIM4 is available as release 1.0.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file ESIM4-1.0.0.tar.gz HMMER +(EMBOSS version of HMMER 2.1.1 - PLEASE USE HMMERNEW) Application details +and documentation for HMMER + +HMMER is available as release 2.1.1 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.1.1.tar.gz HMMERNEW +(EMBOSS version of HMMER 2.3.2) Application details and documentation +for HMMERNEW + +HMMER 2.3.2 is available from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.3.2.tar.gz +MEME (previous EMBOSS version of MEME 2.3.1) Application details and +documentation for MEME + +MEME is available as release 2.3.1 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEME-2.3.1.tar.gz MEMENEW +(EMBOSS version of MEME 3.0.14) Application details and documentation +for MEMENEW which wraps release 3.0.14 of the Meme package + +MEMENEW is available as release 0.1.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEMENEW-0.1.0.tar.gz +MSE (A Multiple Sequence Screen Editor for Biological Sequences.) +Application details and documentation for MSE + +MSE is available as release 1.0.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file MSE-1.0.0.tar.gz MYEMBOSS +(For sites to build their own applications) Application details and +documentation for MYEMBOSS + +MYEMBOSS provides a directory structure and makefile stubs for developing +your own applications more easily than in versions before 3.0.0. + +MYEMBOSS requires autoconf, automake and libtool to be installed. See +the INSTALL file for more informations. + +MYEMBOSS is available as release 1.0.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file MYEMBOSS-1.0.0.tar.gz PHYLIP +(Phylogeny Inference Package) Application details and documentation for +PHYLIP and PHYLIPNEW. + +PHYLIP 3.572 was available as an EMBASSY package with previous +releases. From 3.0.0 we are including a beta test conversion of PHYLIP +3.61 (PHYLIPNEW). Program names now begin with 'f' rather than 'e' +and interfaces are more EMBOSS-like. Please pass on feedback to our bug +reporting list emboss-bug@emboss.open-bio.org + +PHYLIPNEW is available as a Beta release 3.6b from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIP-3.6b.tar.gz TOPO +(Transmembrane display) Application details and documentation for TOPO + +TOPO is available as release 1.0.0 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file TOPO-1.0.0.tar.gz Vienna +RNA package Application details and documentation for VIENNA + +Vienna is available as release 1.6 from our FTP server +ftp://emboss.open-bio.org/pub/EMBOSS/ in file VIENNA-1.6.tar.gz diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild new file mode 100644 index 0000000000000..6a4d1b27940cc --- /dev/null +++ b/academic/EMBASSY/EMBASSY.SlackBuild @@ -0,0 +1,494 @@ +#!/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=${VERSION:-6.4.0} # Keep this the same as the version of EMBOSS. +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -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 $PRGNAM-$VERSION +mkdir $TMP/$PRGNAM-$VERSION + +# Build CBSTOOLS +cd $TMP/$PRGNAM-$VERSION +tar xvf $CWD/CBSTOOLS-*.tar.gz +cd CBSTOOLS-* +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/MEME \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/MSE \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +# 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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \ + --build=$ARCH-slackware-linux +make +make DESTDIR=$PKG install + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/CONTENTS > $PKG/usr/doc/$PRGNAM-$VERSION/CONTENTS + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/EMBASSY/EMBASSY.info b/academic/EMBASSY/EMBASSY.info new file mode 100644 index 0000000000000..b3175501f2bc6 --- /dev/null +++ b/academic/EMBASSY/EMBASSY.info @@ -0,0 +1,44 @@ +PRGNAM="EMBASSY" +VERSION="6.4.0" +HOMEPAGE="http://emboss.sourceforge.net/embassy/" +DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-0.2.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.0.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSS-6.4.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSSDEMO-6.4.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.tar.gz" +MD5SUM="2fe662f0af318cb8875bec734456286d \ + c22e7669a6ca2cfa5c44e08774e69d88 \ + 06a46135fe82aa67d366f51a7228dc54 \ + 7ace7fb34d8f232e53006c8ba0efb7f5 \ + f3deb5b13a3290ce2ca662561e279ea1 \ + d39265e6143c961d2610c76693644fc4 \ + f5cbcb0c04c8d61720a02ec5ff8200bb \ + 3d112bc9a22aa4e925a08fd9eee00485 \ + 4088463d7a84651e9b8693c97ca29428 \ + 3f221816b6db57b9a853b42985780ee9 \ + faa80f5dcdd07751240853d3e34200e5 \ + 0e7aec2815857b71914f36873c14e71d \ + a35ae3fd2ddd06f95f6ce82dca224b07 \ + faa381608b65da74b990d4fc52e8c340 \ + d8893c98eba597ae711a13cb588ecc2e \ + 911c621054c2ed147b5ac8d2e2230c9c \ + c5132cc232fa930286fefc1241bc57c7 \ + cc67545f95f15224926113a2bd3c38ad" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/EMBASSY/README b/academic/EMBASSY/README new file mode 100644 index 0000000000000..a147799664f5d --- /dev/null +++ b/academic/EMBASSY/README @@ -0,0 +1,23 @@ +EMBASSY package includes applications with the same look and feel as +EMBOSS applications, but which the author wishes to be kept separate +from EMBOSS. This is usually because the packages are for specialised +sequence analysis or for non-sequence based analysis, or are licensed +differently to EMBOSS (i.e. non GPL). + +EMBASSY includes the following applications: + +- DOMAINATRIX +- DOMALIGN +- DOMSEARCH +- PHYLIP +- HMMER +- EMNU +- ESIM4 +- MEME +- SIGNATURE +- STRUCTURE +- TOPO +- MSE +- VIENNA + +This requires EMBOSS. diff --git a/academic/EMBASSY/slack-desc b/academic/EMBASSY/slack-desc new file mode 100644 index 0000000000000..329780b6a13ed --- /dev/null +++ b/academic/EMBASSY/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 ':'. + + |-----handy-ruler------------------------------------------------------| +EMBASSY: EMBASSY (EMBOSS associated software) +EMBASSY: +EMBASSY: EMBASSY packages include applications with the same look and feel +EMBASSY: as EMBOSS applications, but which the author wishes to be kept +EMBASSY: separate from EMBOSS. +EMBASSY: +EMBASSY: +EMBASSY: +EMBASSY: +EMBASSY: +EMBASSY: Home: http://emboss.sourceforge.net/embassy/ |