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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($version_parts[2]) >= 4) {
print " BUCKy version check passed.\n";
return;
}
99.scripts/miscs/raxml.sh
Regular → Executable
+1 -1
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@@ -16,5 +16,5 @@ mkdir -p "$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 $params" >/dev/null
99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh
+1 -1
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@@ -1,7 +1,7 @@
#! /bin/bash
set -e
SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
THREADS=${THREADS:-4}
THREADS=${THREADS:-3}
if [ "$#" -ne 3 ]; then
echo "Usage: $0 <in_dir> <out_dir> <ext>"
99.scripts/workflow/phylogeny_reconstruction/03.snaq.jl
+4 -4
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@@ -13,13 +13,13 @@
# Running SNaQ Analysis
using PhyloNetworks, SNaQ;
using Distributed;
addprocs(5);
addprocs(9);
@everywhere using PhyloNetworks, SNaQ;
nruns = 100; # number of runs for each hmax
astralfile = joinpath("..", "..", "species_tree", "aster.out");
astralfile = joinpath("..", "species_tree", "coal.tre");
astraltree = readnewick(astralfile);
### Reading RAxML gene trees and ASTRAL species tree
### Reading RAxML gene trees and ASTRAL species tree
### running in raxml_snaq/ folder
# raxmltrees = joinpath("..", "..", "species_tree", "all.trees");
# inputCF = readtrees2CF(raxmltrees);
@@ -31,7 +31,7 @@ astraltree = readnewick(astralfile);
### Alternatively, reading in the input files from Bucky
### running in input_snaq/ folder
inputCFfile = joinpath("bucky_1.CFs.csv");
inputCFfile = joinpath("..","bucky","bucky_1","input.mb.CFs.csv");
inputCF = readtableCF(inputCFfile);
net0 = snaq!(astraltree, inputCF, hmax=0, filename="net0", seed=123, outgroup="Zju", runs=nruns);
net1 = snaq!(net0, inputCF, hmax=1, filename="net1", seed=123, outgroup="Zju", runs=nruns);