[med-svn] [Git][med-team/minimap2][master] 6 commits: Linking problem has solved somehow

Tue Jun 23 21:08:42 BST 2020


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 <tille at debian.org>  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 <tille at debian.org>  Wed, 13 May 2020 11:44:53 +0200
+ -- Andreas Tille <tille at debian.org>  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 <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 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
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