[med-svn] [Git][med-team/ivar][master] 6 commits: Syntax

Andreas Tille gitlab at salsa.debian.org
Wed May 13 13:57:51 BST 2020 


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 <tille at debian.org>  Wed, 13 May 2020 12:04:45 +0200
+ -- Andreas Tille <tille at debian.org>  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
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