Name: pxftools
Owner: PhenoPackets
Description: A command line utility for operating over Phenotype eXchange Format (PXF) files.
Created: 2016-04-07 14:27:00.0
Updated: 2017-05-01 08:24:12.0
Pushed: 2016-07-28 19:43:22.0
Homepage: null
Size: 68
Language: Scala
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This project provides a command line utility for operating over Phenotype eXchange Format (PXF) files.
Install sbt
(Scala Build Tool) on your system. For Mac OS X, it is easily done using Homebrew: brew install sbt
. sbt
requires a working Java installation, but you do not need to otherwise install Scala.
sbt compile
Development versions of pxftools may depend on the latest snapshot version of the PhenoPackets Java API. You may need to install the latest phenopackets-api
into your local Maven repository before building pxftools.
You can download a prepackaged release.
To build the command-line executable, run:
sbt stage
You will find executables for Unix and Windows in target/universal/stage/bin/
. These depend on the libraries in target/universal/stage/lib
.
sbt universal:packageZipTarball
The release package will be at target/universal/pxftools-<version>.tgz
e
tools [options] command [command options]
ons
-informat=STRING : Input format. By default both yaml and json will be attempted. Set the input format to one of:
yaml
json
hpo-phenote
-out=STRING : Output file. Omit to write to standard out.
-outformat=STRING : Output format. Set the output format to one of:
yaml
json
turtle
ands
onvert <infile> : Read in a PXF file and output in the specified format.
erge <files> ... : Read in multiple PXF files and output as a single merged PXF file in the specified format.