20251217

.gitignore

@@ -13,7 +13,6 @@
 98.results/*
 99.scripts/bucky/
 99.scripts/phyparts/
-.pueue.yml
 run.status
 !*/_description.md
 tmp/

.pueue.yml

@@ -0,0 +1,34 @@
+client:
+  restart_in_place: true
+  read_local_logs: true
+  show_confirmation_questions: false
+  edit_mode: toml
+  show_expanded_aliases: false
+  dark_mode: false
+  max_status_lines: null
+  status_time_format: '%H:%M:%S'
+  status_datetime_format: |-
+    %Y-%m-%d
+    %H:%M:%S
+daemon:
+  pause_group_on_failure: false
+  pause_all_on_failure: false
+  compress_state_file: false
+  callback: /home/ywtang/bin/pueue-ntfy "{{ id }}" "{{ command }}" "{{ path }}" "{{ result }}"
+  env_vars: {}
+  callback_log_lines: 10
+  shell_command: null
+shared:
+  pueue_directory: /home/ywtang/project/biyelunwen/.pueue
+  runtime_directory: null
+  alias_file: null
+  use_unix_socket: true
+  unix_socket_path: null
+  unix_socket_permissions: 448
+  host: 127.0.0.1
+  port: '6924'
+  pid_path: null
+  daemon_cert: /home/ywtang/project/biyelunwen/.pueue/certs/daemon.cert
+  daemon_key: /home/ywtang/project/biyelunwen/.pueue/certs/daemon.key
+  shared_secret_path: /home/ywtang/project/biyelunwen/.pueue/shared_secret
+profiles: {}

slides/20251213/pages/技术路线.md

@@ -45,7 +45,7 @@ end
 
 subgraph subgraph2[Step2. 同源基因集聚类]
     direction LR
-    ass[转录本]:::warn --> CDS[预测CDS，抽取最长转录本的最长ORF作为输入CDS，TransDecoder]:::done
+    ass[转录本]:::warn --> CDS[预测CDS，抽取最长转录本的最长ORF作为输入CDS，TD2]:::done
     CDS --> reducedCDS[单样本CDS序列去冗余，CD-HIT]:::done
     reducedCDS --> ortho[基因家族聚类得到低拷贝同源基因集，OrthoFinder]:::done
     ortho --> homolog[将枣的同源基因整合到低拷贝同源基因集中, hmmer]:::done
@@ -53,7 +53,7 @@ end
 
 subgraph subgraph3[Step3. 基因集筛选与基因树]
     direction LR
-    homo[低拷贝同源基因集]:::warn --> alignment[基于蛋白序列比对，mafft/pal2nal<br>修剪比对序列，trimAl]:::done
+    homo[低拷贝同源基因集]:::warn --> alignment[基于蛋白序列比对，macse<br>修剪比对序列，trimAl]:::done
     alignment --> treeshrink[fasttree快速构树，基于长枝吸引（treeshrink）和比对序列长度过滤基因集]:::done
     treeshrink --> modeltest[序列进化模型检验，modeltest-ng]:::done
     modeltest --> raxml[构建ML单基因树]:::done