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更新脚本和配置，修复 BUCKy 版本检查逻辑，调整 RAxML 脚本参数，增加 cairosvg 依赖，并更新 pixi.lock 文件以反映新依赖。

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agent
2025-12-24 09:00:15 +08:00
parent e467d67723
commit 316017a575
7 changed files with 83 additions and 12 deletions
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99.scripts/miscs/bucky.pl
+4 -4
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@@ -1452,16 +1452,16 @@ sub check_bucky_version {
die " Error determining BUCKy version.\n" if (!@version_parts);
# Check that version is >= 1.4.4
if (defined($version_parts[0]) && $version_parts[0] > 1) {
if (defined($version_parts[0]) && int($version_parts[0]) > 1) {
print " BUCKy version check passed.\n";
return;
}
elsif ((defined($version_parts[0]) && $version_parts[0] == 1) && (defined($version_parts[1]) && $version_parts[1] > 4)) {
elsif ((defined($version_parts[0]) && int($version_parts[0]) == 1) && (defined($version_parts[1]) && int($version_parts[1]) > 4)) {
print " BUCKy version check passed.\n";
return;
}
elsif (((defined($version_parts[0]) && $version_parts[0] == 1) && (defined($version_parts[1]) && $version_parts[1] == 4))
&& defined($version_parts[2]) && $version_parts[2] >= 4) {
elsif (((defined($version_parts[0]) && int($version_parts[0]) == 1) && (defined($version_parts[1]) && int($version_parts[1]) == 4))
&& defined($version_parts[2]) && int($version_parts[2]) >= 4) {
print " BUCKy version check passed.\n";
return;
}
99.scripts/miscs/raxml.sh
Regular → Executable
+1 -1
View File
@@ -16,5 +16,5 @@ mkdir -p "$outdir"
modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
# run raxml-ng
cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
params="--blopt nr_safe --all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
bash -c "$cmd $params" >/dev/null