Andreas Tille pushed to branch master at Debian Med / assembly-stats
Commits:
90cb8ffe by Andreas Tille at 2020-06-09T21:35:16+02:00
Add autopkgtest
- - - - -
866f4f50 by Andreas Tille at 2020-06-09T21:38:16+02:00
Add manpage
- - - - -
36c091b6 by Andreas Tille at 2020-06-09T21:56:57+02:00
Upload to new
- - - - -
8 changed files:
- + debian/assembly-stats.1
- debian/changelog
- + debian/createmanpages
- + debian/docs
- + debian/examples
- + debian/manpages
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/assembly-stats.1
=====================================
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH ASSEMBLY-STATS "1" "June 2020" "assembly-stats 1.0.1+ds" "User Commands"
+.SH NAME
+assembly-stats \- get assembly statistics from FASTA and FASTQ files
+.SH SYNOPSIS
+.B stats
+[options] <list of fasta/q files>
+.SH DESCRIPTION
+Reports sequence length statistics from fasta and/or fastq files
+.SH OPTIONS
+\fB\-l\fR <int>
+.IP
+Minimum length cutoff for each sequence.
+Sequences shorter than the cutoff will be ignored [1]
+.PP
+\fB\-s\fR
+.IP
+Print 'grep friendly' output
+.PP
+\fB\-t\fR
+.IP
+Print tab\-delimited output
+.PP
+\fB\-u\fR
+.IP
+Print tab\-delimited output with no header line
+.PP
+\fB\-v\fR
+.IP
+Print version 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 @@
-assembly-stats (1.0.1+ds-1) UNRELEASED; urgency=medium
+assembly-stats (1.0.1+ds-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #962549)
- -- Andreas Tille <ti...@debian.org> Tue, 09 Jun 2020 17:55:07 +0200
+ -- Andreas Tille <ti...@debian.org> Tue, 09 Jun 2020 21:50:58 +0200
=====================================
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/docs
=====================================
@@ -0,0 +1,4 @@
+README*
+AUTHORS
+debian/tests/run-unit-test
+debian/README.test
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+test_files/*
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/rules
=====================================
@@ -4,24 +4,12 @@
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,$(DEB_BUILD_OPTIONS)))
-# do_stuff_for_testing
-#endif
+override_dh_auto_install:
+ dh_install obj-$(DEB_BUILD_GNU_TYPE)/assembly-stats usr/bin
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,14 +1,11 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=assembly-stats
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # Double quote below to expand the temporary directory variable now versus
- # later is on purpose.
- # shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
@@ -16,4 +13,5 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-#do_stuff_to_test_package#
+assembly-stats fasta_unittest.fasta fastq_unittest.fastq
+assembly-stats filetype_unittest.fasta filetype_unittest.fastq
View it on GitLab:
https://salsa.debian.org/med-team/assembly-stats/-/compare/2a0fd43d7a931036820174c5c582a068c7dd5050...36c091b6b588dd4bacfc070e86a00313ec7007b9
--
View it on GitLab:
https://salsa.debian.org/med-team/assembly-stats/-/compare/2a0fd43d7a931036820174c5c582a068c7dd5050...36c091b6b588dd4bacfc070e86a00313ec7007b9
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