4a7f99d55d
Part of: https://github.com/NixOS/nixpkgs/issues/108938 meta = with stdenv.lib; is a widely used pattern. We want to slowly remove the `stdenv.lib` indirection and encourage people to use `lib` directly. Thus let’s start with the meta field. This used a rewriting script to mostly automatically replace all occurances of this pattern, and add the `lib` argument to the package header if it doesn’t exist yet. The script in its current form is available at https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
42 lines
2.1 KiB
Nix
42 lines
2.1 KiB
Nix
{ lib, stdenv, fetchurl, coreutils, fltk, libjpeg }:
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stdenv.mkDerivation rec {
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version = "5.0.4";
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pname = "seaview";
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src = fetchurl {
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url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
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sha256 = "09yp8467h49qnj7gg0mbcdha4ai3bn6vgs00gb76dd6h3pzfflz1";
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};
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buildInputs = [ fltk libjpeg ];
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patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${coreutils}/bin/rm'#' seaview.cxx";
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installPhase = "mkdir -p $out/bin; cp seaview $out/bin";
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meta = with lib; {
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description = "GUI for molecular phylogeny";
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longDescription = ''
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SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
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- SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
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- SeaView drives programs muscle or Clustal Omega for multiple sequence alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.
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- Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.
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- SeaView computes phylogenetic trees by
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+ parsimony, using PHYLIP's dnapars/protpars algorithm,
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+ distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,
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+ maximum likelihood, driving program PhyML 3.1.
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- Seaview can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees.
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- SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.
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- SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.
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Seaview is published in:
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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.
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'';
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homepage = "http://doua.prabi.fr/software/seaview";
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license = licenses.gpl3;
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maintainers = [ maintainers.iimog ];
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platforms = platforms.linux;
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};
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}
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