diff --git a/.gitignore b/.gitignore index a7f4139..8215a70 100644 --- a/.gitignore +++ b/.gitignore @@ -13,7 +13,6 @@ 98.results/* 99.scripts/bucky/ 99.scripts/phyparts/ -.pueue.yml run.status !*/_description.md -tmp/ \ No newline at end of file +tmp/ diff --git a/.pueue.yml b/.pueue.yml new file mode 100644 index 0000000..a1787c9 --- /dev/null +++ b/.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: {} diff --git a/slides/20251213/pages/技术路线.md b/slides/20251213/pages/技术路线.md index 7f78ab4..b1831e3 100644 --- a/slides/20251213/pages/技术路线.md +++ b/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
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
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