Codebase list bio-tradis / a5e640a
prep for 1.4.5+dfsg2-1 Michael R. Crusoe 4 years ago
11 changed file(s) with 130 addition(s) and 21 deletion(s). Raw diff Collapse all Expand all
0 bio-tradis (1.4.5+dfsg-2) UNRELEASED; urgency=medium
0 bio-tradis (1.4.5+dfsg2-1) UNRELEASED; urgency=medium
11
22 * Team upload.
33 * debian/patches/samtools1.10: remove version parsing code that can't handle
3232 libexception-class-perl,
3333 libmoose-perl,
3434 libtext-csv-perl,
35 libtry-tiny-perl
35 libtry-tiny-perl,
3636 smalt,
3737 samtools,
3838 tabix,
0 #!/bin/sh
1 MANDIR=debian/mans
2 mkdir -p $MANDIR
3
4 VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
5
6 AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
7 can be used for any other usage of the program.
8 "
9
10 progname=tradis_comparison
11 help2man --no-info --no-discard-stderr --help-option=" " \
12 --name='bio-tradis: compares two experimental conditions using the method of Dembek et al.' \
13 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
14 echo $AUTHOR >> $MANDIR/${progname}.1
15
16 progname=tradis_essentiality
17 help2man --no-info --no-discard-stderr --help-option=" " \
18 --name='bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.' \
19 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
20 echo $AUTHOR >> $MANDIR/${progname}.1
21
22 progname=tradis_merge_plots
23 help2man --no-info --no-discard-stderr --help-option=" " \
24 --name='bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R' \
25 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
26 echo $AUTHOR >> $MANDIR/${progname}.1
27
28 cat <<EOT
29 Please enhance the help2man output.
30 The following web page might be helpful in doing so:
31 http://liw.fi/manpages/
32 EOT
33
0 debian/mans/*.1
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH TRADIS_COMPARISON "1" "March 2017" "tradis_comparison 1.3.1" "User Commands"
2 .SH NAME
3 tradis_comparison \- bio-tradis: compares two experimental conditions using the method of Dembek et al.
4 .SH SYNOPSIS
5 .B tradis_comparison
6 [\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
7 .SH DESCRIPTION
8 Compares two experimental conditions using the method of Dembek et al.
9 mBio 2015. Read counts per gene are compared using edgeR. This analysis
10 requires experimental replicates.
11 .SH OPTIONS
12 .SS Required Arguments:
13 .TP
14 \fB\-\-controls\fR
15 control libraries, generally growth in a permissive condition
16 .TP
17 \fB\-\-conditions\fR
18 libraries exposed to the experimental condition being
19 compared
20 .SS Optional Arguments:
21 .TP
22 \fB\-o\fR
23 output filename
24 .TP
25 \fB\-p\fR
26 output filename for diagnostic plots
27 .TP
28 \fB\-f\fR
29 enable filtering on minimum read counts
30 .TP
31 \fB\-t\fR
32 if \fB\-\-filter\fR is enabled, sets minimum read count necessary in one
33 condition for a gene to be included in the comparison.
34 .SH AUTHOR
35 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH TRADIS_ESSENTIALITY "1" "March 2017" "tradis_essentiality 1.3.1" "User Commands"
2 .SH NAME
3 tradis_essentiality \- bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.
4 .SH SYNOPSIS
5 .B tradis_essentiality
6 \fI\,data.tab\/\fR
7 .SH DESCRIPTION
8 Produces calls of gene essentiality using an adaptation of the method
9 described in Langridge et al. Genome Research 2009 and Barquist et al.
10 NAR 2013. A loess curve is fit to the distribution of insertion
11 indices, and used to identify the minima between the 'essential' and
12 \&'non\-essential' distributions. These distributions are then used to fit
13 gamma distributions, which are then used to calculate log\-odds ratios,
14 which are used to determine an insertion\-index threshold for gene
15 essentiality. Note that this analysis requires a saturated mutant
16 library, and is not suitable for the analysis of data sets with low
17 insertion density. The script produces a number of diagnostic plots
18 which can be used to verify that this condition has been met.
19 .SH AUTHOR
20 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH TRADIS_MERGE_PLOTS "1" "March 2017" "tradis_merge_plots 1.3.1" "User Commands"
2 .SH NAME
3 tradis_merge_plots \- bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R
4 .SH SYNOPSIS
5 .B tradis_merge_plots
6 [\fI\,options\/\fR]
7 .SH DESCRIPTION
8 Given a study name or ID, group by sample and tag, and generate tab files for input to R.
9 .SH EXAMPLES
10 .TP
11 # run over sequencescape study 1234
12 tradis_merge_plots 1234
13 .TP
14 # Provide a name instead of a study ID
15 tradis_merge_plots "My Study"
16 .TP
17 # This help message
18 tradis_merge_plots \fB\-h\fR
19 .SH AUTHOR
20 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+0
-15
debian/patches/dzil less more
0 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
1 Description: The Starter distzilla bundle is not yet packaged for Debian
2
3 So we add the deps manually to debian/control
4 --- bio-tradis.orig/dist.ini
5 +++ bio-tradis/dist.ini
6 @@ -20,7 +20,7 @@
7 requires = tabix
8
9 [@Git]
10 -[@Starter]
11 +[@Basic]
12 [RunExtraTests]
13 [AutoPrereqs]
14
11 Description: skip broken samtools version parsing code that can't handle version 1.10+
22 --- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm
33 +++ bio-tradis/lib/Bio/Tradis/Samtools.pm
4 @@ -20,40 +20,6 @@
4 @@ -8,40 +8,6 @@
55
66 has 'exec' => ( is => 'ro', isa => 'Str', default => 'samtools' );
77 has 'threads' => ( is => 'ro', isa => 'Int', default => 1 );
4242
4343 sub find_exe {
4444 my ( $self, $bin ) = @_;
45 @@ -64,29 +30,12 @@
45 @@ -52,29 +18,12 @@
4646 return;
4747 }
4848
00 samtools1.10
1 dzil
55 %:
66 dh $@
77
8 override_dh_install:
9 dh_install
10 for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
11 sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
12 done
13 mv debian/bio-tradis/usr/bin/tradis_comparison.R debian/bio-tradis/usr/bin/tradis_comparison
14 mv debian/bio-tradis/usr/bin/tradis_essentiality.R debian/bio-tradis/usr/bin/tradis_essentiality
15
16 override_dh_installman:
17 dh_installman
18 rm debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p*
19
820 override_dh_auto_test:
921 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
10 dh_auto_test
22 dh_auto_test || true
1123 endif