debian/C-Sibelia.py.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH C-SIBELIA.PY "1" "February 2019" "C-Sibelia.py 3.0.7+ds" "User Commands"
+.SH NAME
+C-Sibelia.py \- comparing two microbial genomes
+.SH DESCRIPTION
+usage: C\-Sibelia.py [\-h] [\-s PARAMETERS] [\-m MINBLOCKSIZE] [\-p PROCESSCOUNT]
+.TP
+[\-i MAXITERATIONS] [\-\-maf MAF] [\-v VARIANT] [\-u UNMAPPED]
+[\-\-debug] [\-t TEMPDIR | \fB\-o\fR OUTDIR]
+reference assembly
+.PP
+A tool for comparing two microbial genomes.
+.SS "positional arguments:"
+.TP
+reference
+A multi\-FASTA file with the reference genome
+.TP
+assembly
+A multi\-FASTA file with the assembly genome
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-s\fR PARAMETERS, \fB\-\-parameters\fR PARAMETERS
+Parameters set, used for the simplification. Option
+"loose" produces fewer blocks, but they are larger
+("fine" is opposite). (default: fine)
+.TP
+\fB\-m\fR MINBLOCKSIZE, \fB\-\-minblocksize\fR MINBLOCKSIZE
+Minimum size of a synteny block (default: 500)
+.TP
+\fB\-p\fR PROCESSCOUNT, \fB\-\-processcount\fR PROCESSCOUNT
+Number of running processes (default: 1)
+.TP
+\fB\-i\fR MAXITERATIONS, \fB\-\-maxiterations\fR MAXITERATIONS
+Maximum number of iterations during a stage of
+simplification (default: 4)
+.TP
+\fB\-\-maf\fR MAF
+Output file for storing alignments in MAF format
+(default: None)
+.TP
+\fB\-v\fR VARIANT, \fB\-\-variant\fR VARIANT
+Output file with detected variants (default:
+variant.vcf)
+.TP
+\fB\-u\fR UNMAPPED, \fB\-\-unmapped\fR UNMAPPED
+Output file for storing unmapped insertions in text
+format (default: None)
+.TP
+\fB\-\-debug\fR
+Generate output in text files (default: False)
+.TP
+\fB\-t\fR TEMPDIR, \fB\-\-tempdir\fR TEMPDIR
+Directory for temporary files (default: None)
+.TP
+\fB\-o\fR OUTDIR, \fB\-\-outdir\fR OUTDIR
+Directory for synteny block output files (default:
+None)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/Sibelia.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH SIBELIA "1" "February 2019" "Sibelia 3.0.7+ds" "User Commands"
+.SH NAME
+Sibelia \- comparative genomics tool
+.SH DESCRIPTION
+USAGE:
+.TP
+Sibelia
+{\-s <loose|fine|far>|\-k <file name>} [\-o <dir name>]
+[\-\-noblocks] [\-r] [\-a] [\-m <integer>] [\-q] [\-g] [\-v] [\-t <dir
+name>] [\-\-lastk <integer > 1>] [\-\-allstages] [\-\-gff]
+[\-\-nopostprocess] [\-\-correctboundaries] [\-i <integer > 0>] [\-\-]
+[\-\-version] [\-h] <fasta files with genomes> ...
+.PP
+Where:
+.HP
+\fB\-s\fR <loose|fine|far>,  \fB\-\-parameters\fR <loose|fine|far>
+.TP
+(OR required)
+Parameters set, used for the simplification. Option
+.IP
+"loose" produces fewer blocks, but they are larger ("fine" is
+opposite).
+.HP
+\fB\-\-\fR OR \fB\-\-\fR
+.HP
+\fB\-k\fR <file name>,  \fB\-\-stagefile\fR <file name>
+.TP
+(OR required)
+File that contains manually chosen simplifications
+.IP
+parameters. See USAGE file for more information.
+.HP
+\fB\-o\fR <dir name>,  \fB\-\-outdir\fR <dir name>
+.IP
+Directory where output files are written
+.HP
+\fB\-\-noblocks\fR
+.IP
+Do not compute synteny blocks
+.HP
+\fB\-r\fR,  \fB\-\-inram\fR
+.IP
+Perform all computations in RAM, don't create temp files.
+.HP
+\fB\-a\fR,  \fB\-\-sharedonly\fR
+.IP
+Output only blocks that occur exactly once in each input sequence.
+.HP
+\fB\-m\fR <integer>,  \fB\-\-minblocksize\fR <integer>
+.IP
+Minimum size of a synteny block, default value = 5000 BP.
+.HP
+\fB\-q\fR,  \fB\-\-sequencesfile\fR
+.IP
+Output sequences of synteny blocks (FASTA format).
+.HP
+\fB\-g\fR,  \fB\-\-graphfile\fR
+.IP
+Output resulting condensed de Bruijn graph (in dot format).
+.HP
+\fB\-v\fR,  \fB\-\-visualize\fR
+.IP
+Draw circos diagram with blocks at different stages.
+.HP
+\fB\-t\fR <dir name>,  \fB\-\-tempdir\fR <dir name>
+.IP
+Directory where temporary files are stored.
+.HP
+\fB\-\-lastk\fR <integer > 1>
+.IP
+Value of K used for the synteny blocks inferring.
+.HP
+\fB\-\-allstages\fR
+.IP
+Output coordinates of synteny blocks from all stages
+.HP
+\fB\-\-gff\fR
+.IP
+Use GFF format for reporting blocks coordinates
+.HP
+\fB\-\-nopostprocess\fR
+.IP
+Do not perform postprocessing (stripe gluing).
+.HP
+\fB\-\-correctboundaries\fR
+.IP
+Correct boundaries of unique synteny blocks.
+.HP
+\fB\-i\fR <integer > 0>,  \fB\-\-maxiterations\fR <integer > 0>
+.IP
+Maximum number of iterations during a stage of simplification, default
+= 4.
+.HP
+\fB\-\-\fR,  \fB\-\-ignore_rest\fR
+.IP
+Ignores the rest of the labeled arguments following this flag.
+.HP
+\fB\-\-version\fR
+.IP
+Displays version information and exits.
+.HP
+\fB\-h\fR,  \fB\-\-help\fR
+.IP
+Displays usage information and exits.
+.TP
+<fasta files with genomes>
+(accepted multiple times)
+.TP
+(required)
+FASTA file(s) with nucleotide sequences.
+.IP
+Program for finding syteny blocks in closely related genomes
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/changelog

 sibelia (3.0.7+ds-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
+    As long as we have no official snpeff package I do not intend to
+    package this.
 
  -- Andreas Tille <tille@debian.org>  Thu, 14 Feb 2019 14:52:05 +0100

debian/createmanpages

+#!/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\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=Sibelia
+help2man --no-info --no-discard-stderr \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=C-Sibelia.py
+help2man --no-info --no-discard-stderr \
+         --name="comparing two microbial genomes" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=snpEffAnnotate.py
+help2man --no-info --no-discard-stderr \
+         --name="Script for variants annotation" \
+            --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/lintian-overrides

 # see https://lists.debian.org/debian-med/2018/06/msg00043.html
 sibelia: script-with-language-extension usr/bin/*.*
+# this file should not be there in an official package - so just ignore the wrong place for now
+sibelia: jar-not-in-usr-share usr/lib/Sibelia/snpEff/snpEff.jar

debian/manpages

+debian/*.1

debian/patches/use_debian_packaged_lagan.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
+Description: Use Debian packaged lagan
+
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
 @@ -27,8 +27,6 @@ else()

debian/patches/use_debian_packaged_libdivsufsort.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
+Description: Use Debian packaged libdivsufsort
+
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
 @@ -1,13 +1,12 @@

debian/rules

@@ -4,18 +4,19 @@
 export LC_ALL=C.UTF-8
 
 include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
 
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@ --sourcedirectory=src
+
+override_dh_installdocs:
+	dh_installdocs
+	mv debian/$(DEB_SOURCE)/usr/share/Sibelia/doc/* debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)
+	rmdir debian/$(DEB_SOURCE)/usr/share/Sibelia/doc
+	dh_link usr/share/doc/$(DEB_SOURCE) usr/share/Sibelia/doc
+
+override_dh_install:
+	dh_install
+	find debian -name LICENSE.txt -delete
+	find debian -name INSTALL.md -delete

debian/snpEffAnnotate.py.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH SNPEFFANNOTATE.PY "1" "February 2019" "snpEffAnnotate.py 3.0.7+ds" "User Commands"
+.SH NAME
+snpEffAnnotate.py \- Script for variants annotation
+.SH DESCRIPTION
+usage: snpEffAnnotate.py [\-h] [\-i SOURCE] [\-o DEST] [\-\-db DB] [\-c CONFIG]
+.PP
+Script for variants annotation
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR SOURCE
+source vcf file with variants
+.TP
+\fB\-o\fR DEST
+destination directory for annotated variants file
+.TP
+\fB\-\-db\fR DB
+snpEff database name
+.TP
+\fB\-c\fR CONFIG
+config file for snpEff
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.