mirror of
https://github.com/NixOS/nixpkgs.git
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4f0dadbf38
After final improvements to the official formatter implementation,
this commit now performs the first treewide reformat of Nix files using it.
This is part of the implementation of RFC 166.
Only "inactive" files are reformatted, meaning only files that
aren't being touched by any PR with activity in the past 2 months.
This is to avoid conflicts for PRs that might soon be merged.
Later we can do a full treewide reformat to get the rest,
which should not cause as many conflicts.
A CI check has already been running for some time to ensure that new and
already-formatted files are formatted, so the files being reformatted here
should also stay formatted.
This commit was automatically created and can be verified using
nix-build a08b3a4d19.tar.gz \
--argstr baseRev b32a094368
result/bin/apply-formatting $NIXPKGS_PATH
53 lines
2.2 KiB
Nix
53 lines
2.2 KiB
Nix
{
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lib,
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stdenv,
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fetchurl,
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coreutils,
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fltk,
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libjpeg,
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}:
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stdenv.mkDerivation rec {
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version = "5.0.5";
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pname = "seaview";
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src = fetchurl {
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url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
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sha256 = "sha256-zo9emLpHiDv6kekbx55NOibxWN2Zg7XngzGkUqSx+PI=";
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};
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buildInputs = [
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fltk
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libjpeg
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];
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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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mainProgram = "seaview";
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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 = "https://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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