Andreas Tille pushed to branch master at Debian Med / minimap2
Commits: 222a4cae by Andreas Tille at 2020-06-23T21:39:49+02:00 Linking problem has solved somehow - - - - - 07e9849e by Andreas Tille at 2020-06-23T21:40:10+02:00 routine-update: debhelper-compat 13 - - - - - 61dba084 by Andreas Tille at 2020-06-23T21:45:51+02:00 Install usr/bin/minimap2.py - - - - - 9ab11ffc by Andreas Tille at 2020-06-23T21:51:11+02:00 Upload to unstable - - - - - 67a2d904 by Andreas Tille at 2020-06-23T21:58:04+02:00 Add lintian-override - - - - - b476e661 by Andreas Tille at 2020-06-23T22:02:57+02:00 Manpage for minimap2.py - - - - - 8 changed files: - debian/changelog - debian/control - + debian/createmanpages - + debian/minimap2.py.1 - debian/python3-mappy.install - + debian/python3-mappy.lintian-overrides - + debian/python3-mappy.manpages - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,13 +1,16 @@ -minimap2 (2.17+dfsg-10) UNRELEASED; urgency=medium +minimap2 (2.17+dfsg-11) UNRELEASED; urgency=medium + + * Add lintian-override + * Manpage for minimap2.py + + -- Andreas Tille <[email protected]> Tue, 23 Jun 2020 21:57:44 +0200 + +minimap2 (2.17+dfsg-10) unstable; urgency=medium * Provide Python3 interface - TODO: https://salsa.debian.org/med-team/ksw2 - >>> import mappy - Traceback (most recent call last): - File "<stdin>", line 1, in <module> - ImportError: /usr/lib/python3/dist-packages/mappy.cpython-38-x86_64-linux-gnu.so: undefined symbol: ksw_extz2_sse + * debhelper-compat 13 (routine-update) - -- Andreas Tille <[email protected]> Wed, 13 May 2020 11:44:53 +0200 + -- Andreas Tille <[email protected]> Tue, 23 Jun 2020 21:40:16 +0200 minimap2 (2.17+dfsg-9) unstable; urgency=medium ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, cython3, python3-all-dev, ===================================== 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 $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=minimap2.py +help2man --no-info --no-discard-stderr --help-option=" " \ + --name="minimap2 Python3 interface" \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +echo "$MANDIR/*.1" > debian/python3-mappy.manpages + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT ===================================== debian/minimap2.py.1 ===================================== @@ -0,0 +1,32 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15. +.TH MINIMAP2.PY "1" "June 2020" "minimap2.py 2.17" "User Commands" +.SH NAME +minimap2.py \- minimap2 Python3 interface +.SH SYNOPSIS +.B minimap2.py +[\fI\,options\/\fR] \fI\,<ref.fa>|<ref.mmi> <query.fq>\/\fR +.SH OPTIONS +.TP +\fB\-x\fR STR +preset: sr, map\-pb, map\-ont, asm5, asm10 or splice +.TP +\fB\-n\fR INT +mininum number of minimizers +.TP +\fB\-m\fR INT +mininum chaining score +.TP +\fB\-k\fR INT +k\-mer length +.TP +\fB\-w\fR INT +minimizer window length +.TP +\fB\-r\fR INT +band width +.TP +\fB\-c\fR +output the cs tag +.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/python3-mappy.install ===================================== @@ -1 +1,2 @@ -/usr/lib/python3* +usr/lib/python3* +usr/bin/minimap2.py \ No newline at end of file ===================================== debian/python3-mappy.lintian-overrides ===================================== @@ -0,0 +1,2 @@ +# see https://lists.debian.org/debian-med/2018/06/msg00043.html +python3-mappy: script-with-language-extension usr/bin/*.* ===================================== debian/python3-mappy.manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/rules ===================================== @@ -52,3 +52,6 @@ override_dh_auto_clean: rm -f MT-human.mmi rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf rm -f libminimap2.a + +override_dh_installman: + dh_installman --language=C View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/compare/0917da2e1c651338bdfab83a0f69cc356001a2f1...b476e661af1d9e7404020308da49e793486bb883 -- View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/compare/0917da2e1c651338bdfab83a0f69cc356001a2f1...b476e661af1d9e7404020308da49e793486bb883 You're receiving this email because of your account on salsa.debian.org.
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