debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: mindthegap
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
-           scan-copyrights
-         **** available in cme + lib-config-model-dpkg-perl     ****
-         **** package a try.  For existing copyright files try  ****
-           cme update dpkg-copyright
+Source: https://github.com/GATB/MindTheGap
+Comment:
 
 Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2014 GATB <gatb.inria.fr>
+License: GNU Affero General Public License v3.0
 
 Files: debian/*
 Copyright: 2019 Shayan Doust <hello@shayandoust.me>
-License: <license>
+License: GNU Affero General Public License v3.0

debian/doc-base

-Document: mindthegap
-Title: <title for this doc>
-Author: <author of this doc>
-Abstract: <if you have no better clue the short and
- long description from debian/control might fit here as well>
-Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
-
-# pick one of the below options
-Format: Text
-Files: /usr/share/doc/mindthegap/<pkg>.txt.gz
-
-Format: html
-Index: /usr/share/doc/mindthegap/html/index.html
-Files: /usr/share/doc/mindthegap/html/*
-
-Format: pdf
-Files: /usr/share/doc/mindthegap/<pkg>.pdf.gz
-
-Format: postscript
-Files: /usr/share/doc/mindthegap/<pkg>.ps.gz

debian/manpages

+debian/mans/*.1

debian/mans/mindthegap.1

+.TH MINDTHEGAP 1
+.SH NAME
+MindTheGap - Perform detection and assembly of DNA insertion variants
+.SH SYNOPSIS
+.B MindTheGap
+<module> [module options]
+.SH DESCRIPTION
+MindTheGap is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detected insertion sites, the other is the set of assembled insertions for each breakpoint.
+
+MindTheGap can also be used as a genome assembly finishing tool: it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file.
+.br
+\X'ps:'\c
+.br
+find - insertion breakpoint detection. 
+.br
+Usage:
+.B MindTheGap
+find ( -in 
+.I <reads.fq>
+| -graph
+.I <graph.h5>
+) -ref
+.I <reference.fa>
+[option]
+.br
+\X'ps:'\c
+.br
+fill - gap-filler or insertion assembly
+.br
+Usage:
+.B MindTheGap
+fill ( -in 
+.I <reads.fq>
+| -graph
+.I <graph.h5>
+) ( -bkpt 
+.I <breakpoints.fa>
+| -contig
+.I <contig.fa>
+) [options]
+.SH COMMON OPTIONS
+help - display the MindTheGap help menu
+.br
+Usage:
+.B MindTheGap
+-help
+.br
+\X'ps:'\c
+.br
+version - display current version
+.br
+Usage:
+.B MindTheGap
+-version