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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。

This commit is contained in:
IvisTang 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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3
.envrc
View File

@ -2,7 +2,6 @@ set +u
export PROJECTHOME="/home/ywtang/project/biyelunwen"
export SCRIPTS="$PROJECTHOME/99.scripts"
export PUEUE_CONFIG_PATH="$PROJECTHOME/.pueue.yml"
watch_file pixi.lock
watch_file pixi.lock
eval "$(pixi shell-hook)"
PATH_add $SCRIPTS/bucky/bin
PATH_add $SCRIPTS/ticr

8
99.scripts/miscs/bucky.pl
View File

@ -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;
}

2
99.scripts/miscs/raxml.sh Normal file → Executable file
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

2
99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh
View File

@ -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>"

8
99.scripts/workflow/phylogeny_reconstruction/03.snaq.jl
View File

@ -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);

71
pixi.lock generated
View File

@ -153,6 +153,8 @@ environments:
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairocffi-1.7.1-pyhd8ed1ab_1.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairosvg-2.8.2-pyhd8ed1ab_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/cd-hit-4.8.1-h5ca1c30_13.tar.bz2
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/cdbtools-0.99-h077b44d_12.tar.bz2
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/certifi-2025.11.12-pyhd8ed1ab_0.conda
@ -168,11 +170,13 @@ environments:
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cpp-expected-1.3.1-h171cf75_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cpython-3.11.14-py311hd8ed1ab_2.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cssselect2-0.8.0-pyhd8ed1ab_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/curl-8.17.0-h4e3cde8_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_1.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cyrus-sasl-2.1.28-hd9c7081_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/dbus-1.16.2-h3c4dab8_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/dendropy-5.0.8-pyhdfd78af_1.tar.bz2
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/diamond-2.1.16-h13889ed_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/distro-1.9.0-pyhd8ed1ab_1.conda
@ -737,6 +741,7 @@ environments:
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tbb-devel-2022.3.0-h74b38a2_1.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/td2-1.0.6-pyhdfd78af_0.tar.bz2
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/threadpoolctl-3.6.0-pyhecae5ae_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/tinycss2-1.5.1-pyhcf101f3_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tktable-2.10-h8d826fa_7.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_2.conda
@ -761,6 +766,7 @@ environments:
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/unicodedata2-17.0.0-py311h49ec1c0_1.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/urllib3-2.5.0-pyhd8ed1ab_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/wayland-1.24.0-hd6090a7_1.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_1.conda
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/x265-3.5-h924138e_3.tar.bz2
@ -1950,6 +1956,31 @@ packages:
license: LGPL-2.1-only or MPL-1.1
size: 978114
timestamp: 1741554591855
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairocffi-1.7.1-pyhd8ed1ab_1.conda
sha256: 1f9642b94454fbcb605f5c711c512cea2147246a4e23aa9baddbda5324089c78
md5: 54b7517cb759be8279efe23708528fe5
depends:
- cairo >=1.14
- cffi >=1.1
- python >=3.9
license: BSD-3-Clause
license_family: BSD
size: 67048
timestamp: 1735230077496
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairosvg-2.8.2-pyhd8ed1ab_0.conda
sha256: 7c76dfe182f775ac9b0a92668fdf5a1d8db6b1459b9ac971d90fcb33609294cf
md5: a873c27598843c20dbb200681f49ea96
depends:
- cairocffi
- cssselect2
- defusedxml
- pillow
- python >=3.9
- tinycss2
license: LGPL-3.0-only
license_family: LGPL
size: 44459
timestamp: 1747337159019
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/cd-hit-4.8.1-h5ca1c30_13.tar.bz2
sha256: 8793a98a7c93b9ade5caaa85e6eeccec69d774c197b772a8132373de2d6ce8e1
md5: 8b5beac305bcf38b77be27e0233e4076
@ -2132,6 +2163,17 @@ packages:
license: Python-2.0
size: 47257
timestamp: 1761172995774
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cssselect2-0.8.0-pyhd8ed1ab_0.conda
sha256: 0a6728d77e337fd5b543765b0cd05eda996b63f4ef0c1bb34a02d78a7d123a68
md5: 504bf822bea0f84547fb31e41de19714
depends:
- python >=3.9
- tinycss2
- webencodings
license: BSD-3-Clause
license_family: BSD
size: 20425
timestamp: 1751498485591
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/curl-8.17.0-h4e3cde8_0.conda
sha256: 3fb39c401fbdbaf68b8f25c1d81600d2a771b6467cc5d7c88fbd1e06d8825ee1
md5: a37bd62e2c34797cdb577920b35f3bc5
@ -2196,6 +2238,15 @@ packages:
license_family: GPL
size: 437860
timestamp: 1747855126005
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
sha256: 9717a059677553562a8f38ff07f3b9f61727bd614f505658b0a5ecbcf8df89be
md5: 961b3a227b437d82ad7054484cfa71b2
depends:
- python >=3.6
license: PSF-2.0
license_family: PSF
size: 24062
timestamp: 1615232388757
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/dendropy-5.0.8-pyhdfd78af_1.tar.bz2
sha256: 102790b465893f5a5c4c3fa045f677e23f990ecc6d1b61d240153c3569a5b99f
md5: 0fa94922431d1074792639704d19461d
@ -9579,6 +9630,17 @@ packages:
license_family: BSD
size: 23869
timestamp: 1741878358548
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/tinycss2-1.5.1-pyhcf101f3_0.conda
sha256: 7c803480dbfb8b536b9bf6287fa2aa0a4f970f8c09075694174eb4550a4524cd
md5: c0d0b883e97906f7524e2aac94be0e0d
depends:
- python >=3.10
- webencodings >=0.4
- python
license: BSD-3-Clause
license_family: BSD
size: 30571
timestamp: 1764621508086
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda
sha256: 1544760538a40bcd8ace2b1d8ebe3eb5807ac268641f8acdc18c69c5ebfeaf64
md5: 86bc20552bf46075e3d92b67f089172d
@ -9905,6 +9967,15 @@ packages:
license_family: MIT
size: 329779
timestamp: 1761174273487
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda
sha256: 19ff205e138bb056a46f9e3839935a2e60bd1cf01c8241a5e172a422fed4f9c6
md5: 2841eb5bfc75ce15e9a0054b98dcd64d
depends:
- python >=3.9
license: BSD-3-Clause
license_family: BSD
size: 15496
timestamp: 1733236131358
- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda
sha256: 70df4ac8cca488618458af4705706551cef7e402bac9c2c41dd17148f60cbd1f
md5: 361e96b664eac64a33c20dfd11affbff

1
pixi.toml
View File

@ -51,6 +51,7 @@ mmseqs2 = ">=18.8cc5c,<19"
paml = ">=4.10.9,<5"
beagle-lib = "==3.1.2"
mrbayes = ">=3.2.7,<4"
cairosvg = ">=2.8.2,<3"
[feature.beast.dependencies]
beagle-lib = ">=4.0.1,<5"