debian/changelog

+kmer (0~20150903+r2013-4) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+  * Fix Perl interpreter path
+  * Fix spelling
+
+ -- Andreas Tille <tille@debian.org>  Sun, 05 Aug 2018 05:47:52 +0200
+
 kmer (0~20150903+r2013-3) unstable; urgency=medium
 
   * Rename source package to match upstream name and primary binary package

debian/compat

-10
+11

debian/control

@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif@debian.org>
 Section: science
 Priority: optional
-Build-Depends:
-	debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                dh-exec,
 # For ATAC
                dh-python,
-	python-all-dev,
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmer.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/kmer.git
+               python-all-dev
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/kmer
+Vcs-Git: https://salsa.debian.org/med-team/kmer.git
 Homepage: http://kmer.sourceforge.net
 
 Package: kmer
@@ -20,7 +19,7 @@ Depends: ${misc:Depends},
          meryl,
          leaff,
          sim4db,
-	 atac,
+         atac
 Description: suite of tools for DNA sequence analysis
  The kmer package is a suite of tools for DNA sequence analysis.
  It provides tools for searching (ESTs, mRNAs, sequencing reads);
@@ -117,15 +116,14 @@ Description: batch spliced alignment of cDNA sequences to a target genome
 
 Package: atac
 Architecture: any
-Depends:
-	${shlibs:Depends},
+Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python:Depends},
          ${perl:Depends},
          libfile-which-perl,
          leaff,
          meryl,
-	gnuplot,
+         gnuplot
 Description: genome assembly-to-assembly comparison
  atac computes a one-to-one pairwise alignment of large DNA sequences. It first
  finds the unique k-mers in each sequence, chains them to larger blocks, and

debian/patches/series

 allow-freebsd-build.patch
 atac-helper-script-paths.patch
 atac-readme.patch
+spelling.patch

debian/patches/spelling.patch

+Description: Fix spelling
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 05 Aug 2018 05:47:52 +0200
+
+--- a/libutil/bitPackedFile.C
++++ b/libutil/bitPackedFile.C
+@@ -157,7 +157,7 @@ bitPackedFile::bitPackedFile(char const
+     } else if ((at == uint64Swap(ac)) && (bt == uint64Swap(bc))) {
+       endianess_flipped = true;
+     } else {
+-      fprintf(stderr, "bitPackedFile::bitPackedFile()-- '%s' looked like a bitPackedFile, but failed the endianess check, not opened.\n", _name);
++      fprintf(stderr, "bitPackedFile::bitPackedFile()-- '%s' looked like a bitPackedFile, but failed the endianness check, not opened.\n", _name);
+       exit(1);
+     }
+   } else {
+--- a/libkmer/driver-existDB.C
++++ b/libkmer/driver-existDB.C
+@@ -178,7 +178,7 @@ const char *usage =
+ "\n"
+ "       -testexhaustive some.fasta some.meryl\n"
+ "         -- Build an existDB table from some.fasta, check _EVERY_ mer\n"
+-"            for existance.  Complain if a mer exists in the table but\n"
++"            for existence.  Complain if a mer exists in the table but\n"
+ "            not in the meryl database.  Assumes 'some.meryl' is the\n"
+ "            mercount of some.fasta.\n"
+ "\n";
+--- a/libutil/palloc.c
++++ b/libutil/palloc.c
+@@ -133,7 +133,7 @@ palloc2(size_t size, void *handle) {
+     root->_cn = root->_nl;
+ 
+     if (root->_dbg > 0)
+-      fprintf(stderr, "palloc()-- Inital block of "sizetFMT" bytes at %p.\n", root->_bs, root->_cn);
++      fprintf(stderr, "palloc()-- Initial block of "sizetFMT" bytes at %p.\n", root->_bs, root->_cn);
+ 
+     root->_cn->_cp = 0;
+     root->_cn->_dt = (char *)really_allocate(root->_bs);
+--- a/sim4dbutils/parseSNP.C
++++ b/sim4dbutils/parseSNP.C
+@@ -491,7 +491,7 @@ main(int argc, char **argv) {
+     fprintf(stderr, "                                 default, and if posTag is not found.\n");
+     fprintf(stderr, "\n");
+     fprintf(stderr, "                                 TAGS: The number immediately after the first\n");
+-    fprintf(stderr, "                                 occurance of the tag will be used.\n");
++    fprintf(stderr, "                                 occurrence of the tag will be used.\n");
+     fprintf(stderr, "\n");
+     fprintf(stderr, "             -o offset           An additive offset to the SNP position.\n");
+     fprintf(stderr, "                                 The default is 0.\n");

debian/rules

@@ -34,5 +34,11 @@ override_dh_auto_clean:
 	$(MAKE) real-clean
 	rm -rf installdir
 
+override_dh_install:
+	dh_install
+	for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \
+	    sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \
+	done
+
 get-orig-source:
 	DEB_VERSION_UPSTREAM=$(DEB_VERSION_UPSTREAM) debian/get-orig-source