[med-svn] [Git][med-team/tiddit][master] 2 commits: Install script

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / tiddit


Commits:
dfc5a253 by Andreas Tille at 2020-05-27T10:56:17+02:00
Install script

- - - - -
cbb65ee3 by Andreas Tille at 2020-05-27T10:59:15+02:00
Add manpage

- - - - -


6 changed files:

- + debian/TIDDIT.py.1
- + debian/createmanpages
- + debian/install
- + debian/lintian-overrides
- + debian/manpages
- debian/rules


Changes:

=====================================
debian/TIDDIT.py.1
=====================================
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH TIDDIT.PY "1" "May 2020" "TIDDIT.py 2.11.0" "User Commands"
+.SH NAME
+TIDDIT.py \- structural variant calling
+.SH SYNOPSIS
+.B TIDDIT.py
+[\-\-sv] [\-\-cov]
+.SH DESCRIPTION
+TIDDIT is a tool to used to identify chromosomal rearrangements using
+Mate Pair or Paired End sequencing data. TIDDIT identifies intra and inter-
+chromosomal translocations, deletions, tandem-duplications and
+inversions, using supplementary alignments as well as discordant pairs.
+.P
+TIDDIT has two analysis modules. The sv mode, which is used to search
+for structural variants. And the cov mode that analyse the read depth of
+a bam file and generates a coverage report.
+.SH OPTIONS
+.TP
+\fB\-\-sv\fR
+call structural variation
+.TP
+\fB\-\-cov\fR
+generate a coverage bed file
+.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/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 $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=TIDDIT.py
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$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/install
=====================================
@@ -0,0 +1 @@
+TIDDIT.py	usr/bin


=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+tiddit: script-with-language-extension usr/bin/*.*


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/rules
=====================================
@@ -4,7 +4,7 @@
 export LC_ALL=C.UTF-8
 
 # for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@ --with python3 --buildsystem=cmake
@@ -21,6 +21,9 @@ override_dh_auto_install:
 	dh_auto_install
 	dh_auto_install --sourcedirectory=src --buildsystem=pybuild
 
+override_dh_python3:
+	dh_python3 --shebang=/usr/bin/python3
+
 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
 #override_dh_auto_test:
 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))



View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/367c6e78664672861465841c91b892965575b101...cbb65ee3fe05970ad7254a6070ef67b97117fab1

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/367c6e78664672861465841c91b892965575b101...cbb65ee3fe05970ad7254a6070ef67b97117fab1
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