diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/seaview/README | 36 | ||||
| -rw-r--r-- | academic/seaview/seaview.SlackBuild | 10 | ||||
| -rw-r--r-- | academic/seaview/seaview.info | 8 |
3 files changed, 29 insertions, 25 deletions
diff --git a/academic/seaview/README b/academic/seaview/README index 21de5ab1c5..7b3a2aa174 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -1,32 +1,32 @@ -SeaView is a multiplatform, graphical user interface for multiple +SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. Important features are: -1) SeaView reads and writes various file formats (NEXUS, MSF, - CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences +1) SeaView reads and writes various file formats (NEXUS, MSF, + CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. - -2) SeaView drives programs muscle or clustalw for multiple sequence - alignment, and also allows to use any external alignment algorithm + +2) SeaView drives programs muscle or clustalw for multiple sequence + alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files. - -3) Seaview drives the Gblocks program to select blocks of + +3) Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites. - + 4) SeaView computes phylogenetic trees by a) parsimony, using PHYLIP's dnapars/protpars algorithm, - b) distance, with NJ or BioNJ algorithms on a variety of + b) distance, with NJ or BioNJ algorithms on a variety of evolutionary distances, c) maximum likelihood, driving program PhyML 3.0. - + 5) SeaView draws phylogenetic trees on screen, PDF or PostScript files -6) SeaView allows to download sequences from EMBL/GenBank/UniProt +6) SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet. For details and citation: -Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a -multiplatform graphical user interface for sequence alignment and -phylogenetic tree building. Molecular Biology and Evolution -27(2):221-224. +Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a +multiplatform graphical user interface for sequence alignment and +phylogenetic tree building. Molecular Biology and Evolution +27(2):221-224. -This requires fltk as a build dependency, but you also need clustalw, -Gblocks, PhyML, and muscle, all of which SeaView drives. +This requires fltk13. You will also need clustalw, Gblocks, PhyML, and +muscle, all of which SeaView drives. diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index ed40b4786e..7a0404d3de 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -24,8 +24,8 @@ # Thanks to Niels Horn for correcting the CFLAGS. -PRGNAM=seaview -VERSION=${VERSION:-4.3.3} +PRGNAM=seaview +VERSION=${VERSION:-4.3.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -40,7 +40,7 @@ fi CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} +OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i486" ]; then SLKCFLAGS="-O2 -march=i486 -mtune=i686" @@ -73,6 +73,10 @@ find . \ # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "14 c FLTK = /usr/include/fltk13" Makefile +sed -i "s:#IFLTK:IFLTK:" Makefile +sed -i "18 c LFLTK = -L/usr/lib${LIBDIRSUFFIX}/fltk13" Makefile +sed -i "28 a LDFLAGS= -Wl,--rpath,/usr/lib${LIBDIRSUFFIX}/fltk13" Makefile # Point to the correct documentation path and phyml executable name sed -i "s:#HELPFILE:HELPFILE:" Makefile diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index c18d48a0ec..dd7ab75b0b 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,10 +1,10 @@ PRGNAM="seaview" -VERSION="4.3.3" +VERSION="4.3.4" HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" -DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.3.tar.gz" -MD5SUM="bee7f73988777721d7596535df8c2594" +DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.4.tar.gz" +MD5SUM="78098f9ea74655edbf8c8dae1d296340" DOWNLOAD_x86_64="" MD5SUM_x86_64="" MAINTAINER="Petar Petrov" EMAIL="ppetrov@paju.oulu.fi" -APPROVED="rworkman" +APPROVED="dsomero" |