debian/changelog

-discosnp (2.4.3-1) UNRELEASED; urgency=medium
+discosnp (2.4.3-1) unstable; urgency=medium
 
   [ Steffen Moeller ]
   * New upstream version
@@ -13,7 +13,7 @@ discosnp (2.4.3-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/changelog (routine-update)
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
 
- -- Andreas Tille <tille@debian.org>  Mon, 27 Jan 2020 14:14:13 +0100
+ -- Andreas Tille <tille@debian.org>  Mon, 27 Jan 2020 15:59:28 +0100
 
 discosnp (2.3.0-3) unstable; urgency=medium
 

debian/install

 scripts			usr/share/discosnp
+discoSnpRAD		usr/share/discosnp
 run_discoSnp*.sh	usr/bin
-discoSnpRAD		usr/bin

debian/lintian-overrides

 # see https://lists.debian.org/debian-med/2018/06/msg00043.html
-discosnp: script-with-language-extension usr/bin/run_discoSnp++.sh
-discosnp: script-with-language-extension usr/bin/run_discoSnpRad.sh
+discosnp: script-with-language-extension usr/bin/run_*.sh
 # The doc is where it belongs to
-discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/scripts_RAD/README.md
+discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/*/README.md

debian/patches/series

@@ -5,3 +5,4 @@ spelling.patch
 #fix_scripts.patch
 adapt_test_scripts.patch
 2to3.patch
+shell_syntax.patch

debian/patches/shell_syntax.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 27 Jan 2020 15:51:58 +0100
+Description: Fix POSIX shell syntax
+
+--- a/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
++++ b/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
+@@ -13,7 +13,7 @@ bold=`tput bold`
+ reset=`tput sgr0`
+ 
+ 
+-function help {
++help() {
+     echo $reset
+ echo "====================================================="
+ echo "Filtering, clustering per locus and vcf formatting of $rawdiscofile"

debian/rules

@@ -15,9 +15,6 @@ override_dh_install:
 	mv debian/$(DEB_SOURCE)/usr/bin/read_file_names			debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
 	mv debian/$(DEB_SOURCE)/usr/bin/quick_hierarchical_clustering	debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
 	rm -rf debian/$(DEB_SOURCE)/usr/share/discosnp/scripts/jenkins
-	for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \
-	    sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \
-	done
 
 override_dh_installman:
 	dh_installman

debian/tests/run-unit-test

@@ -11,7 +11,7 @@ fi
 cp -a /usr/share/doc/${pkg}/test/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
-gunzip ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent*.gz
+gunzip ref_*.fa.gz
 chmod +x simple_test.sh
 
 ./simple_test.sh