Andreas Tille pushed to branch master at Debian Med / mindthegap
Commits: 993c3758 by Shayan Doust at 2019-07-07T19:23:11Z Add manpage into package - - - - - 1c0e7138 by Shayan Doust at 2019-07-07T20:04:28Z Alter debian/copyright file and remove debian/doc-base till a more concrete documentation exists - - - - - 4 changed files: - debian/copyright - − debian/doc-base - + debian/manpages - + debian/mans/mindthegap.1 Changes: ===================================== debian/copyright ===================================== @@ -1,16 +1,12 @@ 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 <[email protected]> -License: <license> +License: GNU Affero General Public License v3.0 ===================================== debian/doc-base deleted ===================================== @@ -1,20 +0,0 @@ -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 ===================================== @@ -0,0 +1 @@ +debian/mans/*.1 ===================================== debian/mans/mindthegap.1 ===================================== @@ -0,0 +1,54 @@ +.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 View it on GitLab: https://salsa.debian.org/med-team/mindthegap/compare/3264dd3e79a2e044dcb22358ba01b1e66f3c6024...1c0e7138f82b96799827535d081dcaa3d9bce2c4 -- View it on GitLab: https://salsa.debian.org/med-team/mindthegap/compare/3264dd3e79a2e044dcb22358ba01b1e66f3c6024...1c0e7138f82b96799827535d081dcaa3d9bce2c4 You're receiving this email because of your account on salsa.debian.org.
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