<commit_before>{ stdenv, fetchurl, jre, makeWrapper }:

stdenv.mkDerivation rec {
  name = "cytoscape-${version}";
  version = "3.4.0";

  src = fetchurl {
    url = "http://chianti.ucsd.edu/${name}/${name}.tar.gz";
    sha256 = "065fsqa01w7j85nljwwc0677lfw112xphnyn1c4hb04166q082p2";
  };

  buildInputs = [jre makeWrapper];

  installPhase = ''
    mkdir -pv $out/{share,bin}
    cp -Rv * $out/share/

    ln -s $out/share/cytoscape.sh $out/bin/cytoscape

    wrapProgram $out/share/gen_vmoptions.sh \
      --set JAVA_HOME "${jre}" \
      --set JAVA  "${jre}/bin/java"

    chmod +x $out/bin/cytoscape
  '';

  meta = {
    homepage = "http://www.cytoscape.org";
    description = "A general platform for complex network analysis and visualization";
    license = stdenv.lib.licenses.lgpl21;
    maintainers = [stdenv.lib.maintainers.mimadrid];
    platforms = stdenv.lib.platforms.unix;
  };
}<commit_msg>cytoscape: fixed issue with startup script<commit_after>{ stdenv, fetchurl, jre, makeWrapper }:

stdenv.mkDerivation rec {
  name = "cytoscape-${version}";
  version = "3.4.0";

  src = fetchurl {
    url = "http://chianti.ucsd.edu/${name}/${name}.tar.gz";
    sha256 = "065fsqa01w7j85nljwwc0677lfw112xphnyn1c4hb04166q082p2";
  };

  buildInputs = [jre makeWrapper];

  installPhase = ''
    mkdir -pv $out/{share,bin}
    cp -Rv * $out/share/

    ln -s $out/share/cytoscape.sh $out/bin/cytoscape

    wrapProgram $out/share/cytoscape.sh \
      --set JAVA_HOME "${jre}" \
      --set JAVA  "${jre}/bin/java"

    chmod +x $out/bin/cytoscape
  '';

  meta = {
    homepage = "http://www.cytoscape.org";
    description = "A general platform for complex network analysis and visualization";
    license = stdenv.lib.licenses.lgpl21;
    maintainers = [stdenv.lib.maintainers.mimadrid];
    platforms = stdenv.lib.platforms.unix;
  };
}
{'fraction_non_alphanumeric': 0.15447154471544716, 'fraction_numerical': 0.03685636856368564, 'mean_word_length': 3.1205357142857144, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3627130', 'n_tokens_mistral': 778, 'n_tokens_neox': 710, 'n_words': 127}