HybPhyloMaker ‘rapid instructions’ 2023

1. Log in to skirit (skirit.ics.muni.cz aka brno2) MetaCentrum frontend

2. Clone HybPhyloMaker and enter the directory
git clone https://github.com/tomas-fer/HybPhyloMaker
mv HybPhyloMaker/HybSeqSource/ .
cd HybSeqSource
wget https://raw.githubusercontent.com/tomas-fer/HybSeqCourse/master/curcuma_HybSeqProbes_first958.fa
cd ../HybPhyloMaker

3. Copy test dataset
cp -r /storage/projects/botany-uk/HybSeqCourse2023/ .

4. Edit file settings.cfg
nano settings.cfg
location=1
server=brno2
data=HybPhyloMaker/HybSeqCourse2023
tree=FastTree
OUTGROUP="Zingiber-officinale_S242"
probes=curcuma_HybSeqProbes_first958.fa
raxmlperjob=1

5. Prepare pseudoreference
qsub HybPhyloMaker0b_preparereference.sh

6. Install appropriate R packages (and wait until this and previous jobs are finished)
qsub HybPhyloMaker0c_Rsetup_MetaCentrum.sh

7. Filter the raw data
qsub HybPhyloMaker1a_rawprocessParallel.sh

8. Run this submitter created by the previous job (this script submits 35 jobs)
cd HybSeqCourse2023/20filtered/ && ./submitRawProcessJobs.sh && cd ../..

9. Run the summary script (after all jobs are finished)
qsub HybPhyloMaker1a2_rawprocessParallel_summary.sh

10. Map reads to pseudoreference
qsub HybPhyloMaker2a_readmappingParallel.sh

11. Run this submitter created by the previous job (this script submits 35 jobs)
cd HybSeqCourse2023/exons/21mapped_bwa/ && ./submitMappingJobs.sh && cd ../../..

12. Run the summary script (after all jobs are finished)
qsub HybPhyloMaker2a2_readmappingParallel_summary.sh

13. Generate PSLX files
qsub HybPhyloMaker3_generatepslx.sh

14. Copy PSLX files
mkdir pslx_AmomumCourse
cp HybSeqCourse2023/exons/50pslx/*.pslx pslx_AmomumCourse

15. Edit file settings.cfg
nano settings.cfg
otherpslx=HybPhyloMaker/pslx_AmomumCourse

16. Generate exon assemblies
qsub HybPhyloMaker4a_processpslx.sh

17. Filter missing data
qsub HybPhyloMaker5_missingdataremoval.sh

18. Generate FastTree trees
qsub HybPhyloMaker6b_FastTree_for_selected.sh

19. Create tree files
qsub HybPhyloMaker7_roottrees.sh

20. Create diverse species trees (run all three, no need to wait...)
qsub HybPhyloMaker8a_astral.sh
qsub HybPhyloMaker8b_astrid.sh
qsub HybPhyloMaker8c_mrl.sh
qsub HybPhyloMaker8e_concatenatedFastTree.sh

21. After all jobs are finished run these additional scripts
qsub HybPhyloMaker8h_neighbourNetwork.sh
qsub HybPhyloMaker8k_quartetsampling.sh
qsub HybPhyloMaker11_phyparts.sh

22. Create a XLSX-formatted report (no need to wait for previous scripts to finish)
qsub HybPhyloMaker_reports.sh