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Source: pique
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Build-Depends: debhelper-compat (= 13)
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pique
Vcs-Git: https://salsa.debian.org/med-team/pique.git
Homepage: https://github.com/tony-travis/PIQUE/
Rules-Requires-Root: no
Package: pique
Architecture: all
Depends: ${perl:Depends},
${misc:Depends},
r-base-core,
emmax,
plink,
eigensoft,
libreadonly-perl,
libparallel-forkmanager-perl,
libfile-slurp-perl,
r-cran-getopt,
r-cran-forecast,
r-cran-optparse,
r-cran-uroot
Description: software pipeline for performing genome wide association studies
PIQUE is a software pipeline for performing genome wide association
studies (GWAS). The main function of PIQUE is to provide ‘convenience’
wrappers that allow users to perform GWAS using the popular program
EMMAX (Kang et al., 2010) without the need to be familiar with all of
the software tools used to generate the required EMMAX input files.
PIQUE will also perform a number of quality control steps prior to
running EMMAX, ensuring that the various input data files are in the
correct format. PIQUE proceeds in two main stages although there are
multiple entry and exit points from which the pipeline can be run. The
first stage consists of running the “pique-input” program, which can
read genotype and phenotype information in several different formats and
generates all the necessary input files required to run EMMAX. The
second step in the pipeline uses the “pique-run” program to actually run
EMMAX using the files generated by “pique-input” (or pre-existing
user-supplied input files) to perform the GWAS and output the analysis
summary files.
Package: pique-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Enhances: pique
Description: software pipeline for performing genome wide association studies (docs)
PIQUE is a software pipeline for performing genome wide association
studies (GWAS). The main function of PIQUE is to provide ‘convenience’
wrappers that allow users to perform GWAS using the popular program
EMMAX (Kang et al., 2010) without the need to be familiar with all of
the software tools used to generate the required EMMAX input files.
PIQUE will also perform a number of quality control steps prior to
running EMMAX, ensuring that the various input data files are in the
correct format. PIQUE proceeds in two main stages although there are
multiple entry and exit points from which the pipeline can be run. The
first stage consists of running the “pique-input” program, which can
read genotype and phenotype information in several different formats and
generates all the necessary input files required to run EMMAX. The
second step in the pipeline uses the “pique-run” program to actually run
EMMAX using the files generated by “pique-input” (or pre-existing
user-supplied input files) to perform the GWAS and output the analysis
summary files.
.
This package contains the documentation as well as example data.
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