[med-svn] [Git][med-team/pique][master] 5 commits: Add missing Depends
Andreas Tille
gitlab at salsa.debian.org
Mon Jul 20 13:01:47 BST 2020
Andreas Tille pushed to branch master at Debian Med / pique
Commits:
fb07dcae by Andreas Tille at 2020-07-20T12:50:33+02:00
Add missing Depends
- - - - -
6cbd8981 by Andreas Tille at 2020-07-20T13:44:09+02:00
Add manpages
- - - - -
5a32daea by Andreas Tille at 2020-07-20T13:49:23+02:00
create extra doc package
- - - - -
cb0d0d34 by Andreas Tille at 2020-07-20T13:58:36+02:00
Script should somehow work as autopkgtest but its not activated for the moment
- - - - -
0dd6cdbc by Andreas Tille at 2020-07-20T14:01:29+02:00
Fix description
- - - - -
9 changed files:
- debian/control
- + debian/createmanpages
- − debian/docs
- + debian/pique-doc.install
- + debian/pique-input.1
- + debian/pique-run.1
- debian/install → debian/pique.install
- + debian/pique.manpages
- debian/tests/run-unit-test
Changes:
=====================================
debian/control
=====================================
@@ -21,7 +21,9 @@ Depends: ${perl:Depends},
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
@@ -33,10 +35,35 @@ Description: software pipeline for performing genome wide association studies
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 “emmax-input” program, which can
+ 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 “emmax-run” program to actually run
- EMMAX using the files generated by “emmax-input” (or pre-existing
+ 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.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,34 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=pique-input
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=pique-run
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/docs deleted
=====================================
@@ -1 +0,0 @@
-doc/*.odt
=====================================
debian/pique-doc.install
=====================================
@@ -0,0 +1,2 @@
+doc/*.odt usr/share/doc/pique
+test/* usr/share/doc/pique/examples
=====================================
debian/pique-input.1
=====================================
@@ -0,0 +1,55 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH PIQUE-INPUT "1" "July 2020" "pique-input 1.0" "User Commands"
+.SH NAME
+pique-input \- software pipeline for performing genome wide association studies
+.SH SYNOPSIS
+.B pique
+\fI\,-i in_prefix -o out_prefix\/\fR
+[\-d] [\-v] [\-f in_format] [\-k kinship]
+[\-p pheno_file] [\-c covar_file [\-e n_pc]]
+.SH OPTIONS
+.SS Mandatory parameters:
+.HP
+\fB\-i\fR in_prefix: input prefix for the input files
+.HP
+\fB\-o\fR out_prefix: output prefix for the output files
+.SS Optional parameters:
+.HP
+\fB\-d\fR debug: saves intermediate files for debugging
+.HP
+\fB\-v\fR verbose: display all output from plink and smartpca
+.HP
+\fB\-f\fR in_format: input file format (default = ped)
+.IP
+ped = requires in_prefix.ped & in_prefix.map files
+tped = requires in_prefix.tped & in_prefix.tfam files
+vcf = requires .vcf filename
+.HP
+\fB\-p\fR pheno_file: phenotype file name
+.IP
+Defaults to [in_prefix].pheno
+.HP
+\fB\-g\fR group[,group...]: genotype sub\-groups to be analysed
+.HP
+\fB\-n\fR number: minimum number of genotypes in sub\-group (default = 20)
+.HP
+\fB\-k\fR kinship: method to calculate kinship matrix
+.IP
+Either 'IBS' (default) or 'BN' methods
+.HP
+\fB\-c\fR covar_file: generate covariate file [out_prefix].covar
+.IP
+from SNP information in .ped file using smartpca (EIGENSOFT)
+.HP
+\fB\-e\fR n_pc: number of eigenvectors to keep from smartpca
+.HP
+\fB\-m\fR MAF: Minor Allele Frequency
+.HP
+\fB\-x\fR missing: maximum per\-SNP missing
+.PP
+Further details and examples are given in the documentation
+.SH AUTHOR
+Tony Travis <tony.travis at abdn.ac.uk> and Alex Douglas <a.douglas at abdn.ac.uk>
+.PP
+This manpage was written by Andreas Tille for the Debian distribution and
+can be used for any other usage of the program.
=====================================
debian/pique-run.1
=====================================
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH PIQUE-RUN "1" "July 2020" "pique-run 1.0" "User Commands"
+.SH NAME
+pique-run \- software pipeline for performing genome wide association studies
+.SH SYNOPSIS
+.B pique-run
+\fI\,-i in_prefix \/\fR[\fI\,-n threads\/\fR] [\fI\,-o out_prefix\/\fR] [\fI\,-k kinship\/\fR] [\fI\,-c cov_file\/\fR] \fI\,-t transform\/\fR
+.SH OPTIONS
+.SS Mandatory parameters:
+.HP
+\fB\-i\fR in_prefix: input prefix for .tped .tfam and .pheno files
+.SS Optional parameters:
+.HP
+\fB\-n\fR threads: number of threads. Defaults to 1
+.HP
+\fB\-o\fR out_prefix: prefix for output files. Defaults to [input_prefix]
+.HP
+\fB\-k\fR kinship: method used to calculate kinship matrix. Either 'IBS' (default) or 'BN' methods
+.HP
+\fB\-c\fR cov_file: covariate file name
+.HP
+\fB\-t\fR transform: phenotype transformation (BC = Box\-Cox, default = none)
+.PP
+More information about pique\-run usage can be found in the PIQUE documentation
+.SH AUTHOR
+Tony Travis <tony.travis at abdn.ac.uk> and Alex Douglas <a.douglas at abdn.ac.uk
+.PP
+This manpage was written by Andreas Tille for the Debian distribution and
+can be used for any other usage of the program.
=====================================
debian/install → debian/pique.install
=====================================
=====================================
debian/pique.manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,13 +1,10 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=pique
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # Double quote below to expand the temporary directory variable now versus
- # later is on purpose.
- # shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
@@ -15,4 +12,4 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-#do_stuff_to_test_package#
+make
View it on GitLab: https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b
--
View it on GitLab: https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b
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