diff -Nru mummer-3.23+dfsg/debian/changelog mummer-3.23+dfsg/debian/changelog
--- mummer-3.23+dfsg/debian/changelog 2020-04-15 06:37:33.000000000 +0000
+++ mummer-3.23+dfsg/debian/changelog 2020-07-23 18:31:54.000000000 +0000
@@ -1,3 +1,15 @@
+mummer (3.23+dfsg-6) unstable; urgency=medium
+
+ [ Étienne Mollier ]
+ * Team upload.
+ * Removed dependency to C-Shell.
+
+ [ Andreas Tille ]
+ * Remove csh from docs
+ * debhelper-compat (= 13)
+
+ -- Étienne Mollier Thu, 23 Jul 2020 20:31:54 +0200
+
mummer (3.23+dfsg-5) unstable; urgency=medium
[ Charles Plessy ]
diff -Nru mummer-3.23+dfsg/debian/control mummer-3.23+dfsg/debian/control
--- mummer-3.23+dfsg/debian/control 2020-04-15 06:37:33.000000000 +0000
+++ mummer-3.23+dfsg/debian/control 2020-07-23 18:31:54.000000000 +0000
@@ -5,11 +5,10 @@
Charles Plessy
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
texlive-latex-base,
texlive-latex-recommended,
texlive-fonts-recommended,
- csh | c-shell
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/mummer
Vcs-Git: https://salsa.debian.org/med-team/mummer.git
diff -Nru mummer-3.23+dfsg/debian/mummer.docs mummer-3.23+dfsg/debian/mummer.docs
--- mummer-3.23+dfsg/debian/mummer.docs 2020-04-15 06:37:33.000000000 +0000
+++ mummer-3.23+dfsg/debian/mummer.docs 2020-07-23 18:31:54.000000000 +0000
@@ -1,3 +1,3 @@
README
ACKNOWLEDGEMENTS
-debian/NEWS.Debian
+debian/NEWS
diff -Nru mummer-3.23+dfsg/debian/NEWS mummer-3.23+dfsg/debian/NEWS
--- mummer-3.23+dfsg/debian/NEWS 1970-01-01 00:00:00.000000000 +0000
+++ mummer-3.23+dfsg/debian/NEWS 2020-07-23 18:31:54.000000000 +0000
@@ -0,0 +1,11 @@
+mummer (3.23~dfsg-3) unstable; urgency=medium
+
+ This version of mummer contains two patches which are fetched from an old
+ code copy of mummer version 3.20 which is shipped with mugsy (to be
+ packaged). It adds the tools delta2blocks and delta2maf as well as an
+ additional option to mummer's delta-filter tool -b for reporting
+ duplications.
+
+ Please check your results thoroughly to avoid any side effects.
+
+ -- Andreas Tille Mon, 13 Apr 2015 22:29:27 +0200
diff -Nru mummer-3.23+dfsg/debian/NEWS.Debian mummer-3.23+dfsg/debian/NEWS.Debian
--- mummer-3.23+dfsg/debian/NEWS.Debian 2020-04-15 06:37:33.000000000 +0000
+++ mummer-3.23+dfsg/debian/NEWS.Debian 1970-01-01 00:00:00.000000000 +0000
@@ -1,11 +0,0 @@
-mummer (3.23~dfsg-3) unstable; urgency=medium
-
- This version of mummer contains two patches which are fetched from an old
- code copy of mummer version 3.20 which is shipped with mugsy (to be
- packaged). It adds the tools delta2blocks and delta2maf as well as an
- additional option to mummer's delta-filter tool -b for reporting
- duplications.
-
- Please check your results thoroughly to avoid any side effects.
-
- -- Andreas Tille Mon, 13 Apr 2015 22:29:27 +0200
diff -Nru mummer-3.23+dfsg/debian/patches/remove-csh-dependency.patch mummer-3.23+dfsg/debian/patches/remove-csh-dependency.patch
--- mummer-3.23+dfsg/debian/patches/remove-csh-dependency.patch 1970-01-01 00:00:00.000000000 +0000
+++ mummer-3.23+dfsg/debian/patches/remove-csh-dependency.patch 2020-07-23 18:31:54.000000000 +0000
@@ -0,0 +1,39 @@
+Description: remove checks for csh
+ While the package can safely be built without csh, there are still a few
+ checks that are causing various error messages at build time. This patch
+ removes them.
+Author: Étienne Mollier
+Forwarded: no
+Last-Update: 2020-07-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- mummer.orig/Makefile
++++ mummer/Makefile
+@@ -38,7 +38,6 @@
+ CC := $(filter /%,$(shell /bin/sh -c 'type gcc'))
+ CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))
+ SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
+-CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+ AR := $(filter /%,$(shell /bin/sh -c 'type ar'))
+
+@@ -76,9 +75,6 @@
+ ifndef SED
+ @echo "ERROR: 'sed' StreamEDitor not found"
+ endif
+-ifndef CSH
+- @echo "ERROR: 'csh' C-shell not found"
+-endif
+ ifndef PERL
+ @echo "ERROR: 'perl' PERL not found"
+ endif
+--- mummer.orig/scripts/Makefile
++++ mummer/scripts/Makefile
+@@ -18,7 +18,6 @@
+ endif
+
+ SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
+-CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+ VPATH := $(BIN_DIR)
+
diff -Nru mummer-3.23+dfsg/debian/patches/remove-csh-from-doc.patch mummer-3.23+dfsg/debian/patches/remove-csh-from-doc.patch
--- mummer-3.23+dfsg/debian/patches/remove-csh-from-doc.patch 1970-01-01 00:00:00.000000000 +0000
+++ mummer-3.23+dfsg/debian/patches/remove-csh-from-doc.patch 2020-07-23 18:31:54.000000000 +0000
@@ -0,0 +1,96 @@
+Author: Andreas Tille
+Description: Remove csh from docs
+Last-Update: Thu, 23 Jul 2020 20:31:54 +0200
+
+--- a/README
++++ b/README
+@@ -68,7 +68,7 @@ format (qry.seq) type the following at t
+
+ or
+
+- './run-mummer3.csh ref.seq qry.seq '
++ './run-mummer3 ref.seq qry.seq '
+
+ To produce the following files:
+ .out
+--- a/docs/run-mummer1.README
++++ b/docs/run-mummer1.README
+@@ -38,10 +38,10 @@ it crashes for that reason, that's not a
+ required.
+
+ To use this system, first compile it by typing 'make' at the
+-command line. There is a script, 'run-mummer1.csh', that runs all
++command line. There is a script, 'run-mummer1', that runs all
+ the steps of aligning two genomes. The script takes these arguments:
+
+- run-mummer1.csh [-r]
++ run-mummer1 [-r]
+
+ The two genomes must DNA sequences in FASTA format. Multi-FASTA
+ files don't work. The tag is used to create 4 output files,
+@@ -60,7 +60,7 @@ not performed.
+
+ IMPORTANT: the performance of the program can critically depend on the
+ minimum MUM length you use. The default is 20bp. If you want to
+-change it, do the following: edit the file run-mummer1.csh. Add a new
++change it, do the following: edit the file run-mummer1. Add a new
+ length switch to the 'mummer' call.
+
+ The other file - one that we often spend lots of time analyzing - is
+@@ -90,8 +90,8 @@ Files in this directory:
+ gaps.cc Finds longest consistent set of matches in list
+ produced by mummer1 program.
+
+- run-mummer1.csh Script to run alignment programs. Format is:
+- run-mummer1.csh [-flip]
++ run-mummer1 Script to run alignment programs. Format is:
++ run-mummer1 [-flip]
+ will be used to make output files: .out , .gaps
+ and .align . -r will reverse complement
+
+--- a/docs/web/manual/index.html
++++ b/docs/web/manual/index.html
+@@ -516,7 +516,6 @@ td {
+ make (GNU make 3.79.1)
+ perl (PERL 5.6.0)
+ sh (GNU sh 1.14.7)
+- csh (tcsh 6.10.00)
+ g++ (GNU gcc 2.95.3)
+ sed (GNU sed 3.02)
+ awk (GNU awk 3.0.4)
+@@ -647,7 +646,7 @@ td {
+ can also be viewed with the same utility programs (see above). Refer to the
+ PROmer section for a list of options and output descriptions.
+ run-mummer1 and run-mummer3
+-run-mummer1
and run-mummer3
are cshell script pipelines
++
run-mummer1
and run-mummer3
are shell script pipelines
+ for the general alignment of two sequences. They follow the same three steps
+ of NUCmer and PROmer, in that they match, cluster and extend, however they handle
+ any input sequence, not just nucleotide. This non-discrimination can be useful,
+@@ -1192,7 +1191,7 @@ Long Exact Matches:
+ repeat positions are denoted by an 'r'
following the Start2 position,
+ and are relative to the forward strand of the sequence.
+ 5.1.3. exact-tandems
+-exact-tandems
is a wrapper cshell script for the repeat-match
++
exact-tandems
is a wrapper shell script for the repeat-match
+ program. It provides a list of exact tandem repeats within a single input sequence.
+ Command line syntax
+ exact-tandems <sequence file> <min length>
+@@ -1910,7 +1909,7 @@ PROMER
+ and the reverse strand of the query.
+ Program options
+ There are no available command line options for run-mummer1
. Instead,
+- the user must directly edit the csh
script to alter the command
++ the user must directly edit the sh
script to alter the command
+ line values passed to the individual pipeline programs. The only available tweak
+ is changing the minimum match length value for mummer
, set with
+ the -l
option within the script. Decreasing this value may increase
+@@ -2008,7 +2007,7 @@ S: tagctgtcggggcgatcccctcggtagtga
+ requires hand editing the script.
+ Program options
+ There are no available command line options for run-mummer3
. Instead,
+- the user must directly edit the csh
script to alter the command
++ the user must directly edit the sh
script to alter the command
+ line values passed to the individual pipeline programs. Altering these parameters
+ is suggested for most applications, as the default values may not always produce
+ the best output. Parameter values may be added or changed for mummer
,
diff -Nru mummer-3.23+dfsg/debian/patches/series mummer-3.23+dfsg/debian/patches/series
--- mummer-3.23+dfsg/debian/patches/series 2020-04-15 06:37:33.000000000 +0000
+++ mummer-3.23+dfsg/debian/patches/series 2020-07-23 18:31:54.000000000 +0000
@@ -9,3 +9,5 @@
# most probably broken see bug #843621
# addition_from_report_duplicates.patch
mummerplot.patch
+remove-csh-dependency.patch
+remove-csh-from-doc.patch