diff options
Diffstat (limited to 'academic/EMBASSY')
| -rw-r--r-- | academic/EMBASSY/CONTENTS | 122 | ||||
| -rw-r--r-- | academic/EMBASSY/EMBASSY.SlackBuild | 306 | ||||
| -rw-r--r-- | academic/EMBASSY/EMBASSY.info | 74 | ||||
| -rw-r--r-- | academic/EMBASSY/README | 15 | ||||
| -rw-r--r-- | academic/EMBASSY/slack-desc | 2 |
5 files changed, 195 insertions, 324 deletions
diff --git a/academic/EMBASSY/CONTENTS b/academic/EMBASSY/CONTENTS index d739dcfb71..bd0665b82b 100644 --- a/academic/EMBASSY/CONTENTS +++ b/academic/EMBASSY/CONTENTS @@ -1,94 +1,64 @@ -The EMBASSY package includes the following: -------------------------------------------- +CBSTOOLS: The CBSTOOLS package is a set of wrappers to selected +applications from the CBS group in Denmark. -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. +CLUSTALOMEGA: A wrapper for the clustal omega application. -Application details and documentation for DOMAINATRIX +DOMAINATRIX: The DOMAINATRIX programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -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 +DOMALIGN: The DOMALIGN programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -Application details and documentation for DOMALIGN +DOMSEARCH: The DOMSEARCH programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -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 +EMNU: The EMNU package is a simple EMBOSS menu system written by Gary +Williams at HGMP. -Application details and documentation for DOMSEARCH +ESIM4: The ESIM4 package is an EMBOSS conversion of the SIM4 package +from Liliana Florea. -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 +HMMER: A suite of application wrappers to the original hmmer v2.3.2 +applications written by Sean Eddy. hmmer v2.3.2 must be installed on +the same system as EMBOSS and the location of the hmmer executables +must be defined in your path for EMBASSY HMMER to work. -Application details and documentation for SIGNATURE +IPRSCAN: The IPRSCAN package is a wrapper for the interproscan +program. -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 +MEME: The EMBASSY MEME package contains 'wrapper' applications +providing an EMBOSS-style interface to the applications in the +original MEME package version 4.0.0 developed by Timothy L. Bailey. -Application details and documentation for STRUCTURE +MIRA: The MIRA package is a fragment assembly program from Bastien +Chevreux. The program was converted to EMBOSS by Alan Bleasby as two +applications, one for EST assembly and one for shotgun fragment +assembly -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 +MSE: The MSE package is a multiple sequence editor. The program was +contributed to the EMBOSS package by the author, Will Gilbert, as one +of the first EMBASSY programs. -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 +MYEMBOSS: A package for your own software developments. -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 +MYEMBOSSDEMO: The MYEMBOSSDEMO package contains example applications +using EMBOSS data types -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 +PHYLIPNEW: The PHYLIPNEW programs are EMBOSS conversions of the +programs in Joe Felsenstein's PHYLIP package, version 3.69. -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 +SIGNATURE: The SIGNATURE programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -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 +STRUCTURE: The STRUCTURE programs were developed by Jon Ison and +colleagues at MRC HGMP for their protein domain research. They are +included as an EMBASSY package as a work in progress. -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 +TOPO: The TOPO package is a graphics program to display membrane +protein topology by Susan Jean Johns. -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 +VIENNA: These programs are adapted from the VIENNA RNA package. 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 diff --git a/academic/EMBASSY/EMBASSY.info b/academic/EMBASSY/EMBASSY.info index 65685dce3c..49623f8ba1 100644 --- a/academic/EMBASSY/EMBASSY.info +++ b/academic/EMBASSY/EMBASSY.info @@ -1,42 +1,42 @@ PRGNAM="EMBASSY" -VERSION="6.4.0" +VERSION="6.5.7" HOMEPAGE="http://emboss.sourceforge.net/embassy/" -DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/CBSTOOLS-1.0.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/CLUSTALOMEGA-0.2.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/DOMAINATRIX-0.1.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/DOMALIGN-0.1.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/DOMSEARCH-0.1.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/EMNU-1.05.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/ESIM4-1.0.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/HMMER-2.3.2.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/IPRSCAN-4.3.1.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MEME-4.0.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MSE-3.0.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MYEMBOSS-6.4.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MYEMBOSSDEMO-6.4.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/PHYLIPNEW-3.69.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/SIGNATURE-0.1.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/STRUCTURE-0.1.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/TOPO-2.0.0.tar.gz \ - ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/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="ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-0.2.0.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSS-6.5.1.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSSDEMO-6.5.0.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.650.tar.gz \ + ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.650.tar.gz" +MD5SUM="4913776ee5ff93ae839762107f8d8bc8 \ +f24967741eb2fe9c3bccd6458276e127 \ +d7539f6ee6f25bb401ffad2802441010 \ +079a6371390201fa39f19c25cce8d5ba \ +5fd0e943f4db9f9ea008eabd68dc60e7 \ +6e0b7ac797554c52f413d23e5781e71b \ +2ca9069bf9c87697bf52c77b25a659d7 \ +d82017cc68ce3d381e8cc6dcfd68f39e \ +81720978302afc8d855b316651be5b2a \ +4d2dac5a2d66ad43552271be81c1cd1b \ +3b26ecbdf8032680f1de148f5d91d776 \ +54e9ca4dadd0b988f8964f886c6f026c \ +f3cb3421a79e7e6466686628de346b20 \ +488d117d32a391a9b53c60260595e67b \ +361773a6f1b0b862f5cbf3d4d3ee1fa0 \ +40afa99f995f34275005b76f8b05c337 \ +5a0b0c478cece42cc564599b91f9c1cf \ +633c16e28818b0dc4d3ae084a7beae56" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="EMBOSS" diff --git a/academic/EMBASSY/README b/academic/EMBASSY/README index 4e80c801fc..7d462ea3f3 100644 --- a/academic/EMBASSY/README +++ b/academic/EMBASSY/README @@ -1,9 +1,10 @@ -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 +EMBASSY 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 +EMBASSY includes the following: CBSTOOLS, CLUSTALOMEGA, DOMAINATRIX, +DOMALIGN, DOMSEARCH, DOMSEARCH, EMNU, ESIM4, HMMER, IPRSCAN, MEME, +MSE, MYEMBOSS, MYEMBOSSDEMO, PHYLIPNEW, SIGNATURE, STRUCTURE, TOPO and +VIENNA. For a more detailed description check the CONTENTS file. diff --git a/academic/EMBASSY/slack-desc b/academic/EMBASSY/slack-desc index 329780b6a1..407970d319 100644 --- a/academic/EMBASSY/slack-desc +++ b/academic/EMBASSY/slack-desc @@ -12,8 +12,8 @@ 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: Home: http://emboss.sourceforge.net/embassy/ EMBASSY: EMBASSY: EMBASSY: EMBASSY: -EMBASSY: Home: http://emboss.sourceforge.net/embassy/ |