Andreas Tille pushed to branch master at Debian Med / cat-bat
Commits: 99e0ce5b by Andreas Tille at 2020-05-18T16:52:35+02:00 Fix installation, add Depends - - - - - 97476fe0 by Andreas Tille at 2020-05-18T16:57:52+02:00 Add manpage - - - - - a0ae69ff by Andreas Tille at 2020-05-18T17:08:35+02:00 Upload to new - - - - - d88bd680 by Andreas Tille at 2020-05-18T17:11:45+02:00 Fix typo in interpreter line - - - - - 9 changed files: - + debian/CAT.1 - debian/changelog - debian/control - + debian/createmanpages - debian/install - + debian/links - + debian/manpages - + debian/patches/fix_interpreter.patch - + debian/patches/series Changes: ===================================== debian/CAT.1 ===================================== @@ -0,0 +1,39 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15. +.TH CAT "1" "May 2020" "CAT 5.0.4" "User Commands" +.SH NAME +CAT \- tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) +.SH SYNOPSIS +.B CAT +(prepare | contigs | bin | bins | add_names | summarise) [\-v / \fB\-\-version]\fR [\-h / \fB\-\-help]\fR +.SH DESCRIPTION +Run Contig Annotation Tool (CAT) or Bin Annotation Tool (BAT). +.SH OPTIONS +.SS "Required choice:" +.TP +prepare +Download database files and construct databases. +.TP +contigs +Run CAT. +.TP +bin +Run BAT on a single bin. +.TP +bins +Run BAT on a set of bins. +.TP +add_names +Add taxonomic names to CAT or BAT output files. +.TP +summarise +Summarise a named CAT or BAT classification file. +.SS "Optional arguments:" +.TP +\fB\-v\fR, \fB\-\-version\fR +Print version information and exit. +.TP +\fB\-h\fR, \fB\-\-help\fR +Show this help message and exit. +.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 ===================================== @@ -1,5 +1,5 @@ -cat-bat (5.0.4-1) UNRELEASED; urgency=medium +cat-bat (5.0.4-1) unstable; urgency=medium - * Initial release (Closes: #<bug>) + * Initial release (Closes: #960937) - -- Andreas Tille <[email protected]> Mon, 18 May 2020 16:30:46 +0200 + -- Andreas Tille <[email protected]> Mon, 18 May 2020 17:05:20 +0200 ===================================== debian/control ===================================== @@ -14,8 +14,10 @@ Homepage: https://github.com/dutilh/CAT Package: cat-bat Architecture: any Depends: ${python3:Depends}, - ${misc:Depends} -Description: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) + ${misc:Depends}, + diamond-aligner, + prodigal +Description: taxonomic classification of contigs and metagenome-assembled genomes (MAGs) Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown @@ -24,4 +26,4 @@ Description: tool for taxonomic classification of contigs and metagenome-assembl predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files - are formated appropriately + are formatted appropriately. ===================================== debian/createmanpages ===================================== @@ -0,0 +1,28 @@ +#!/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\n \ +This manpage was written by $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=CAT +help2man --no-info --no-discard-stderr --help-option=" -h" \ + --name="$NAME" \ + --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/install ===================================== @@ -1,2 +1 @@ -CAT_pack/*.py usr/share/cat-bat -CAT_pack/CAT usr/bin +CAT_pack/* usr/share/cat-bat ===================================== debian/links ===================================== @@ -0,0 +1,2 @@ +usr/share/cat-bat/CAT usr/bin/CAT + ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/patches/fix_interpreter.patch ===================================== @@ -0,0 +1,12 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Mon, 18 May 2020 17:05:20 +0200 +Description: Fix typo in interpreter line + +--- a/CAT_pack/check.py ++++ b/CAT_pack/check.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env/ python3 ++#!/usr/bin/env python3 + + import datetime + import decimal ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +fix_interpreter.patch View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/compare/76c2f9e92b5ac75ef4089b5d193cfde11dc724b1...d88bd6803ccabda697f75d0ab33e2cc2b4fb510c -- View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/compare/76c2f9e92b5ac75ef4089b5d193cfde11dc724b1...d88bd6803ccabda697f75d0ab33e2cc2b4fb510c You're receiving this email because of your account on salsa.debian.org.
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