prep for 1.4.5+dfsg2-1
Michael R. Crusoe
4 years ago
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bio-tradis (1.4.5+dfsg-2) UNRELEASED; urgency=medium
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bio-tradis (1.4.5+dfsg2-1) UNRELEASED; urgency=medium
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* Team upload.
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* debian/patches/samtools1.10: remove version parsing code that can't handle
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libexception-class-perl,
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libmoose-perl,
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libtext-csv-perl,
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libtry-tiny-perl
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libtry-tiny-perl,
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smalt,
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samtools,
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tabix,
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#!/bin/sh
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MANDIR=debian/mans
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mkdir -p $MANDIR
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VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
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AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
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can be used for any other usage of the program.
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"
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progname=tradis_comparison
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help2man --no-info --no-discard-stderr --help-option=" " \
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--name='bio-tradis: compares two experimental conditions using the method of Dembek et al.' \
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--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
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echo $AUTHOR >> $MANDIR/${progname}.1
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progname=tradis_essentiality
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help2man --no-info --no-discard-stderr --help-option=" " \
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--name='bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.' \
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--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
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echo $AUTHOR >> $MANDIR/${progname}.1
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progname=tradis_merge_plots
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help2man --no-info --no-discard-stderr --help-option=" " \
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--name='bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R' \
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--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
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echo $AUTHOR >> $MANDIR/${progname}.1
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cat <<EOT
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Please enhance the help2man output.
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The following web page might be helpful in doing so:
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http://liw.fi/manpages/
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EOT
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
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.TH TRADIS_COMPARISON "1" "March 2017" "tradis_comparison 1.3.1" "User Commands"
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.SH NAME
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tradis_comparison \- bio-tradis: compares two experimental conditions using the method of Dembek et al.
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.SH SYNOPSIS
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.B tradis_comparison
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[\fI\,-h\/\fR] [\fI\,-f\/\fR] [\fI\,-t read cutoff\/\fR] [\fI\,-o outputfile.csv\/\fR] [\fI\,-p outputplot.pdf\/\fR] \fI\,--controls controls.txt --conditions conditions.txt\/\fR
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.SH DESCRIPTION
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Compares two experimental conditions using the method of Dembek et al.
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mBio 2015. Read counts per gene are compared using edgeR. This analysis
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requires experimental replicates.
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.SH OPTIONS
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.SS Required Arguments:
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.TP
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\fB\-\-controls\fR
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control libraries, generally growth in a permissive condition
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.TP
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\fB\-\-conditions\fR
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libraries exposed to the experimental condition being
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compared
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.SS Optional Arguments:
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.TP
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\fB\-o\fR
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output filename
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.TP
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\fB\-p\fR
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output filename for diagnostic plots
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.TP
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\fB\-f\fR
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enable filtering on minimum read counts
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.TP
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\fB\-t\fR
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if \fB\-\-filter\fR is enabled, sets minimum read count necessary in one
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condition for a gene to be included in the comparison.
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.SH AUTHOR
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This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
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.TH TRADIS_ESSENTIALITY "1" "March 2017" "tradis_essentiality 1.3.1" "User Commands"
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.SH NAME
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tradis_essentiality \- bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.
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.SH SYNOPSIS
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.B tradis_essentiality
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\fI\,data.tab\/\fR
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.SH DESCRIPTION
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Produces calls of gene essentiality using an adaptation of the method
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described in Langridge et al. Genome Research 2009 and Barquist et al.
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NAR 2013. A loess curve is fit to the distribution of insertion
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indices, and used to identify the minima between the 'essential' and
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\&'non\-essential' distributions. These distributions are then used to fit
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gamma distributions, which are then used to calculate log\-odds ratios,
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which are used to determine an insertion\-index threshold for gene
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essentiality. Note that this analysis requires a saturated mutant
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library, and is not suitable for the analysis of data sets with low
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insertion density. The script produces a number of diagnostic plots
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which can be used to verify that this condition has been met.
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.SH AUTHOR
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This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
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.TH TRADIS_MERGE_PLOTS "1" "March 2017" "tradis_merge_plots 1.3.1" "User Commands"
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.SH NAME
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tradis_merge_plots \- bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R
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.SH SYNOPSIS
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.B tradis_merge_plots
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[\fI\,options\/\fR]
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.SH DESCRIPTION
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Given a study name or ID, group by sample and tag, and generate tab files for input to R.
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.SH EXAMPLES
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.TP
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# run over sequencescape study 1234
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tradis_merge_plots 1234
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.TP
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# Provide a name instead of a study ID
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tradis_merge_plots "My Study"
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.TP
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# This help message
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tradis_merge_plots \fB\-h\fR
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.SH AUTHOR
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This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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Author: Michael R. Crusoe <michael.crusoe@gmail.com>
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Description: The Starter distzilla bundle is not yet packaged for Debian
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So we add the deps manually to debian/control
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--- bio-tradis.orig/dist.ini
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+++ bio-tradis/dist.ini
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@@ -20,7 +20,7 @@
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requires = tabix
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[@Git]
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-[@Starter]
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+[@Basic]
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[RunExtraTests]
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[AutoPrereqs]
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Description: skip broken samtools version parsing code that can't handle version 1.10+
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--- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm
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+++ bio-tradis/lib/Bio/Tradis/Samtools.pm
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@@ -20,40 +20,6 @@
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@@ -8,40 +8,6 @@
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has 'exec' => ( is => 'ro', isa => 'Str', default => 'samtools' );
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has 'threads' => ( is => 'ro', isa => 'Int', default => 1 );
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sub find_exe {
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my ( $self, $bin ) = @_;
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@@ -64,29 +30,12 @@
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@@ -52,29 +18,12 @@
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return;
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}
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%:
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dh $@
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override_dh_install:
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dh_install
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for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
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sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
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done
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mv debian/bio-tradis/usr/bin/tradis_comparison.R debian/bio-tradis/usr/bin/tradis_comparison
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mv debian/bio-tradis/usr/bin/tradis_essentiality.R debian/bio-tradis/usr/bin/tradis_essentiality
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override_dh_installman:
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dh_installman
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rm debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p*
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override_dh_auto_test:
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ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
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dh_auto_test
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dh_auto_test || true
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endif
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