pheno-ranker -r <individuals.json> -t <patient.json> [-options]

  Arguments:
    * Cohort mode:
      -r, --reference <file>         BFF/PXF file(s) in JSON or YAML format (array or object)

    * Patient mode:
      -t, --target <file>            BFF/PXF file in JSON or YAML format (object or array of 1 object)

  Options:
    -age                             Include age-related variables; excludes agent-like terms (BFF/PXF-only) [>no-age|age]
    -a, --align [path/basename]      Write alignment file(s). If not specified, default filenames are used [default: alignment.*]
    -append-prefixes <prefixes>      Prefixes for primary_key when #cohorts >= 2 [default: C]
    -config <file>                   YAML config file to modify default parameters [default: share/conf/config.yaml]
    -cytoscape-json [file]           Serializes the pairwise comparison matrix as an undirected graph in JSON, compatible with Cytoscape [default: graph.json]
    -e, --export [path/basename]     Export miscellaneous JSON files. If not specified, default filenames are used [default: export.*]
    -exclude-terms <terms>           Exclude BFF/PXF terms (e.g., --exclude-terms sex, id) or column names in JSON-derived from CSV 
    -graph-stats [file]              Generates a text file with key graph metrics, for use with <-cytoscape-json> [default: graph_stats.txt]
    -include-hpo-ascendants          Include ascendant terms from the Human Phenotype Ontology (HPO)
    -include-terms <terms>           Include BFF/PXF terms (e.g., --include-terms diseases) or column names in JSON-derived from CSV
    -max-number-var <number>         Maximum variables for binary string [default: 10000]
    -max-out <number>                Print only N comparisons [default: 50]
    -o, --out-file <file>            Output file path [default: -r matrix.txt | -t rank.txt]
    -poi, --patients-of-interest <id_list>   Export JSON files for the selected individual IDs during a dry-run
    -poi-out-dir <directory>         Directory for JSON files (used with --poi)
    -similarity-metric-cohort <metric>  Similarity metric for cohort mode [>hamming|jaccard]
    -sort-by <metric>                Sort by Hamming distance or Jaccard index [>hamming|jaccard]
    -w, --weights <file>             YAML file with weights

  Generic Options:
    -debug <level>                   Print debugging (from 1 to 5, being 5 max)
    -h, --help                       Brief help message
    -log                             Save log file [default: pheno-ranker-log.json]
    -man                             Full documentation
    -no-color                        Toggle color output [>color|no-color]
    -v, --verbose                    Verbosity on
    -V, --version                    Print version

sudo apt-get install cpanminus libperl-dev

cpanm --notest --sudo Pheno::Ranker
pheno-ranker -h

cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
cpanm --notest Pheno::Ranker
pheno-ranker --help

echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc

git clone https://github.com/cnag-biomedical-informatics/pheno-ranker.git
cd pheno-ranker

sudo apt-get install cpanminus libperl-dev

cpanm --notest --sudo --installdeps .
bin/pheno-ranker --help            

cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
cpanm --notest --installdeps .
bin/pheno-ranker --help

echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc

sudo apt-get install python3-pip libzbar0
pip3 install -r requirements.txt

docker pull manuelrueda/pheno-ranker:latest
docker image tag manuelrueda/pheno-ranker:latest cnag/pheno-ranker:latest

wget https://raw.githubusercontent.com/cnag-biomedical-informatics/pheno-ranker/main/Dockerfile

# Docker Version 19.03 and Above (Supports buildx)
docker buildx build -t cnag/pheno-ranker:latest .

# Docker Version Older than 19.03 (Does Not Support buildx)
docker build -t cnag/pheno-ranker:latest .

docker run -tid -e USERNAME=root --name pheno-ranker cnag/pheno-ranker:latest

docker exec -ti pheno-ranker bash

/usr/share/pheno-ranker/bin/pheno-ranker

 docker run --user 1000 -tid --name pheno-ranker cnag/pheno-ranker:latest

docker run -tid --volume /media/mrueda/4TBT/data:/data --name pheno-ranker-mount cnag/pheno-ranker:latest

# First I create an alias to simplify invocation (from the host)
alias pheno-ranker='docker exec -ti pheno-ranker-mount /usr/share/pheno-ranker/bin/pheno-ranker'

# Now I use the alias to run the command (note that I use the flag --o to specify the filepath)
pheno-ranker -r /data/individuals.json -o /data/matrix.txt

* Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOS, OpenSUSE) should do as well.
  (It should also work on macOS and Windows Server, but we are only providing information for Linux here)
* Perl 5 (>= 5.26 core; installed by default in most Linux distributions). Check the version with "perl -v".
* >= 4GB of RAM
* 1 core
* At least 16GB HDD

$ ./pheno-ranker -r phenopackets.json  # intra-cohort

$ ./pheno-ranker -r phenopackets.yaml -o my_matrix.txt # intra-cohort

$ ./pheno-ranker -r phenopackets.json -w weights.yaml --exclude-terms sex ethnicity exposures # intra-cohort with weights

$ $path/pheno-ranker -r individuals.json others.yaml --append-prefixes CANCER CONTROL  # inter-cohort

$ $path/pheno-ranker -r individuals.json -t patient.yaml -max-out 100 # mode patient

* Error message: R plotting
    Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 1 did not have X elements
    Calls: as.matrix -> read.table -> scan
    Execution halted
  Solution: Make sure that the values of your primary key (e.g., "id") do not contain spaces (e.g., "my fav id" must be "my_fav_id")

* Error message: Foo
  Solution: Bar