Condor submit files (and executable where applicable)
This submit file executes the fasttree program from the /opt/PepPrograms folder. The "10" in the arguments line specifies the desired number of threads, while the "dummy_snps.fasta" corresponds to the input file (your snp alignment).
condor_submit fasttree.submit
This submit file executes a corresponding bash script (run_parsnp.sh) with three arguments: a compressed folder (.tar.gz) containing the genomes to be assembled (fasta format), the path to the reference genome (stored in opt/data), and the number of threads to use.
condor_submit run_parsnp.submit
This is a simple bash script that will unpack the compressed genomes, make and move them into a directory, execute parsnp, and finally compress parsnp's output (a folder containing various files) so that it can be transferred back.
This submit file runs blastp of files named $(PROCESS).tsv against a blast database (which is transferred with the jobs).
Folder contains three submit files, one for each step of generating a bootstrapped ML tree with RAxML. "bestTree" and "bootstrap" steps can be run at the same time. Threads can differ between jobs. Dag needs to be edited with alignment name, desired output suffixes, and the number of threads. Requested memory and space is based on an alignment of ~600 Mtb samples and may not reflect others needs - please change as needed for your purposes.
condor_submit_dag RAxML.dag
Folder contains submit files to run maximum likelihood tree and bootstrapping with RAxML. Automatically calculates the best protein model for the tree. Input file should be an amino acid alignment. Example DAG is also included.
condor_submit_dag RAxML.dag
Folder contains scripts to run pilon in variant calling mode under the following parameters: --variant --mindepth 10 --minmq 40 --minqual 20. Beginning with your "pipelineIn.txt" file, use the make_pilon_input.py script to generate a file containing one line for each Biosample (SRS/ERS) in your "pipelineIn.txt" file with the runs and strategy (paired == frags, single == unpaired, matepair == jumps) associated with the biosample. Feed this file into the make_ind_pilon.py scripts to generate individual submit and sh files for each biosample. Then submit them to conodor!
Directory contains shell script and submit file to run mugsy. Submit file should be edited to contain file names for your samples. Reference genome is first.