Andreas Tille pushed to branch master at Debian Med / ivar
Commits: 45425cb6 by Andreas Tille at 2020-05-13T14:31:39+02:00 Syntax - - - - - 792f940f by Andreas Tille at 2020-05-13T14:32:26+02:00 Bioconda entry - - - - - 62abd814 by Andreas Tille at 2020-05-13T14:44:45+02:00 hardening - - - - - 39a9c772 by Andreas Tille at 2020-05-13T14:47:04+02:00 doc-base - - - - - 4422e01b by Andreas Tille at 2020-05-13T14:49:02+02:00 Add manpage - - - - - 6f519f38 by Andreas Tille at 2020-05-13T14:51:24+02:00 Upload to new - - - - - 9 changed files: - debian/changelog - debian/copyright - + debian/createmanpages - + debian/ivar-doc.doc-base - + debian/ivar.1 - + debian/ivar.install - + debian/manpages - debian/rules - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,5 @@ -ivar (1.2.2+dfsg-1) UNRELEASED; urgency=medium +ivar (1.2.2+dfsg-1) unstable; urgency=medium - * Initial release (Closes: #<bug>) + * Initial release (Closes: #960509) - -- Andreas Tille <[email protected]> Wed, 13 May 2020 12:04:45 +0200 + -- Andreas Tille <[email protected]> Wed, 13 May 2020 14:51:11 +0200 ===================================== debian/copyright ===================================== @@ -20,7 +20,7 @@ License: GPL-2+ it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. - + . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ===================================== 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 $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=${PROGNAME} +help2man --no-info --no-discard-stderr --help-option=" " \ + --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/ivar-doc.doc-base ===================================== @@ -0,0 +1,16 @@ +Document: ivar-doc +Title: Documentation for iVar +Author: Nathan D Grubaugh, Karthik Gangavarapu, e.a. +Abstract: functions broadly useful for viral amplicon-based sequencing + iVar is a computational package that contains functions broadly useful + for viral amplicon-based sequencing. Additional tools for metagenomic + sequencing are actively being incorporated into iVar. While each of + these functions can be accomplished using existing tools, iVar contains + an intersection of functionality from multiple tools that are required + to call iSNVs and consensus sequences from viral sequencing data across + multiple replicates. +Section: Science/Biology + +Format: html +Index: /usr/share/doc/ivar/html/index.html +Files: /usr/share/doc/ivar/html/* ===================================== debian/ivar.1 ===================================== @@ -0,0 +1,42 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15. +.TH IVAR "1" "May 2020" "ivar 1.2.2" "User Commands" +.SH NAME +ivar \- functions broadly useful for viral amplicon-based sequencing +.SH SYNOPSIS +.B ivar +[\fI\,command <trim|variants|filtervariants|consensus|getmasked|removereads|version|help>\/\fR] +.SH DESCRIPTION +iVar is a computational package that contains functions broadly useful +for viral amplicon-based sequencing. Additional tools for metagenomic +sequencing are actively being incorporated into iVar. While each of +these functions can be accomplished using existing tools, iVar contains +an intersection of functionality from multiple tools that are required +to call iSNVs and consensus sequences from viral sequencing data across +multiple replicates. +.SH COMMANS +.TP +trim +Trim reads in aligned BAM file +.TP +variants +Call variants from aligned BAM file +.TP +filtervariants +Filter variants across replicates or samples +.TP +consensus +Call consensus from aligned BAM file +.TP +getmasked +Detect primer mismatches and get primer indices for the amplicon to be masked +.TP +removereads +Remove reads from trimmed BAM file +.TP +version +Show version information +.PP +To view detailed usage for each command type `ivar <command>` +.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/ivar.install ===================================== @@ -0,0 +1 @@ +usr ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/rules ===================================== @@ -3,29 +3,7 @@ # DH_VERBOSE := 1 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 $@ - -### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected -#override_dh_auto_test: -#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) -# do_stuff_for_testing -#endif - -### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script -#get-orig-source: -# . debian/get-orig-source ===================================== debian/upstream/metadata ===================================== @@ -19,3 +19,6 @@ Reference: PMCID: PMC6325816 URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7 eprint: https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-018-1618-7 +Registry: + - Name: conda:bioconda + Entry: ivar View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/1a6ae93ab11c2f26e41a28e970a14a5ef0767d9d...6f519f38889203822eefa7871b356a0dac09ddf7 -- View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/1a6ae93ab11c2f26e41a28e970a14a5ef0767d9d...6f519f38889203822eefa7871b356a0dac09ddf7 You're receiving this email because of your account on salsa.debian.org.
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