NAME

       phylo_pipeline - Phylo Pipeline of PALEOMIX suite

SYNOPSIS

       paleomix phylo_pipeline <command> [options] [makefiles]

DESCRIPTION

       The  PALEOMIX  pipelines  are  a set of pipelines and tools designed to aid the rapid processing of High-
       Throughput Sequencing (HTS) data: The BAM pipeline  processes  de-multiplexed  reads  from  one  or  more
       samples,  through sequence processing and alignment, to generate BAM alignment files useful in downstream
       analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference  on  BAM  alignment
       files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out
       a  suite  of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in
       archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

       The pipelines have been designed  with  ancient  DNA  (aDNA)  in  mind,  and  includes  several  features
       especially  useful  for  the  analyses  of  ancient  samples, but can all be for the processing of modern
       samples, in order to ensure consistent data processing.

       phylo_pipeline is the phylo pipeline of paleomix(1).

OPTIONS

   Commands
       phylo_pipeline help
              Display this message.

       phylo_pipeline example [...]
              Copy example project to folder.

       phylo_pipeline makefile
              Print makefile template.

       phylo_pipeline genotype [...]
              Carry out genotyping according to makefile.

       phylo_pipeline msa [...]
              Carry out multiple sequence alignment.

       phylo_pipeline phylogeny
              Carry out phylogenetic inference.

   Optional arguments
       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

       --to-dot-file=DOT_FILE
              Write dependency tree to the specified dot-file.

   Progress reporting
       --progress-ui=PROGRESS_UI
              Select method for displaying the progress of the pipeline:  'running'  =  Display  only  currently
              running  nodes;  'progress' = Display changes in state; 'summary'; one-line summary only. [Default
              is 'running']

       --ui-colors=UI_COLORS
              Enable, disable, or force the use of color codes when printing the command-line UI. Unless forced,
              colors will only be printed if STDOUT is a TTY [Default is 'on']

   Logging
       --log-file=LOG_FILE
              Create the specified log-file and write any messages to this file. By default, a log-file will  be
              generated in the folder specified using --temp-root, but only when messages are logged

       --log-level=LOG_LEVEL
              Log  messages  to log-file at and above the specified level; one of 'info', 'warning', 'error', or
              'debug' [warning]

   Scheduling
       --samtools-max-threads=SAMTOOLS_MAX_THREADS
              Maximum number of threads to use when genotyping or building pileups [1]

       --examl-max-threads=EXAML_MAX_THREADS
              Maximum number of threads to use for each instance of ExaML [1]

       --max-threads=MAX_THREADS
              Maximum number of threads to use in total [4]

       --dry-run
              If passed, only a dry-run in performed, the dependency tree is printed, and no tasks are executed.

   Required paths:
       --temp-root=TEMP_ROOT
              Location for temporary files and folders [/tmp/USERNAME/phylo_pipeline]

       --samples-root=SAMPLES_ROOT
              Location of BAM files for each sample [./data/samples]

       --regions-root=REGIONS_ROOT
              Location of BED files containing regions of interest [./data/regions]

       --prefix-root=PREFIX_ROOT
              Location of prefixes (FASTAs) [./data/prefixes]

       --refseq-root=REFSEQ_ROOT
              Location of reference sequences (FASTAs) [./data/refseqs]

       --destination=DESTINATION
              The destination folder for result files [./results]

   Files and executables:
       --list-input-files
              List all input files used by pipeline for the makefile(s), excluding any generated by the pipeline
              itself.

       --list-output-files
              List all output files generated by pipeline for the makefile(s).

       --list-executables
              List all executables required by the pipeline, with version requirements (if any).

   Config files:
       --write-config-file
              Write config using current settings to $HOME/.paleomix/phylo_pipeline.ini

SEE ALSO

       paleomix(1)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

phylo_pipeline 1.2.7                              February 2017                                PHYLO_PIPELINE(1)