debian/changelog

-porechop (0.2.3+dfsg-1) UNRELEASED; urgency=medium
+porechop (0.2.3+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #890112)
 
- -- Andreas Tille <tille@debian.org>  Sun, 26 Aug 2018 19:57:42 +0200
+ -- Andreas Tille <tille@debian.org>  Mon, 27 Aug 2018 10:53:28 +0200

debian/control

@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
                dh-python,
                python3-all-dev,
                libseqan2-dev
-Standards-Version: 4.2.0
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/porechop
 Vcs-Git: https://salsa.debian.org/med-team/porechop.git
 Homepage: https://rrwick.github.io/Porechop

debian/createmanpages

+#!/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: *//'`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr \
+         --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

-porechop/*.py		usr/share/porechop/porechop
-porechop-runner.py	usr/share/porechop
+porechop/*.py		usr/lib/porechop/porechop
+porechop/*.so		usr/lib/porechop/porechop
+porechop-runner.py	usr/lib/porechop

debian/links

-usr/share/porechop/porechop-runner.py	usr/bin/porechop
+usr/lib/porechop/porechop-runner.py	usr/bin/porechop

debian/manpages

+debian/*.1

debian/patches/no_soname.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 26 Aug 2018 19:57:42 +0200
+Origin: https://lists.debian.org/debian-python/2018/08/msg00113.html
+Description: Do not set soname
+
+--- a/Makefile
++++ b/Makefile
+@@ -44,7 +44,7 @@ debug: FLAGS+=$(DEBUGFLAGS)
+ debug: $(TARGET)
+ 
+ $(TARGET): $(OBJECTS)
+-	$(CXX) $(FLAGS) $(CXXFLAGS) $(LDFLAGS) -Wl,$(SONAME),$(TARGET) -o $(TARGET) $(OBJECTS)
++	$(CXX) $(FLAGS) $(CXXFLAGS) $(LDFLAGS) -o $(TARGET) $(OBJECTS)
+ 
+ clean:
+ 	$(RM) $(OBJECTS)

debian/patches/series

 add_python_interpreter_line.patch
+no_soname.patch

debian/porechop.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PORECHOP "1" "August 2018" "porechop 0.2.3" "User Commands"
+.SH NAME
+porechop \- adapter trimmer for Oxford Nanopore reads
+.SH SYNOPSIS
+.B porechop
+[\-h] \fB\-i\fR INPUT [\-o OUTPUT]
+[\-\-format {auto,fasta,fastq,fasta.gz,fastq.gz}] [\-v VERBOSITY]
+[\-t THREADS] [\-\-version] [\-b BARCODE_DIR]
+[\-\-barcode_threshold BARCODE_THRESHOLD]
+[\-\-barcode_diff BARCODE_DIFF] [\-\-require_two_barcodes]
+[\-\-untrimmed] [\-\-discard_unassigned]
+[\-\-adapter_threshold ADAPTER_THRESHOLD]
+[\-\-check_reads CHECK_READS] [\-\-scoring_scheme SCORING_SCHEME]
+[\-\-end_size END_SIZE] [\-\-min_trim_size MIN_TRIM_SIZE]
+[\-\-extra_end_trim EXTRA_END_TRIM]
+[\-\-end_threshold END_THRESHOLD] [\-\-no_split]
+[\-\-discard_middle] [\-\-middle_threshold MIDDLE_THRESHOLD]
+[\-\-extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]
+[\-\-extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE]
+[\-\-min_split_read_size MIN_SPLIT_READ_SIZE]
+.SH DESCRIPTION
+Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them
+from the ends and splitting reads with internal adapters
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "Main options:"
+.TP
+\fB\-i\fR INPUT, \fB\-\-input\fR INPUT
+FASTA/FASTQ of input reads or a directory which will
+be recursively searched for FASTQ files (required)
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+Filename for FASTA or FASTQ of trimmed reads (if not
+set, trimmed reads will be printed to stdout)
+.TP
+\fB\-\-format\fR {auto,fasta,fastq,fasta.gz,fastq.gz}
+Output format for the reads \- if auto, the format
+will be chosen based on the output filename or the
+input read format (default: auto)
+.TP
+\fB\-v\fR VERBOSITY, \fB\-\-verbosity\fR VERBOSITY
+Level of progress information: 0 = none, 1 = some, 2
+= lots, 3 = full \- output will go to stdout if reads
+are saved to a file and stderr if reads are printed
+to stdout (default: 1)
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of threads to use for adapter alignment
+(default: 4)
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.SS "Barcode binning settings:"
+.IP
+Control the binning of reads based on barcodes (i.e. barcode
+demultiplexing)
+.TP
+\fB\-b\fR BARCODE_DIR, \fB\-\-barcode_dir\fR BARCODE_DIR
+Reads will be binned based on their barcode and
+saved to separate files in this directory
+(incompatible with \fB\-\-output\fR)
+.TP
+\fB\-\-barcode_threshold\fR BARCODE_THRESHOLD
+A read must have at least this percent identity to a
+barcode to be binned (default: 75.0)
+.TP
+\fB\-\-barcode_diff\fR BARCODE_DIFF
+If the difference between a read's best barcode
+identity and its second\-best barcode identity is
+less than this value, it will not be put in a
+barcode bin (to exclude cases which are too close to
+call) (default: 5.0)
+.TP
+\fB\-\-require_two_barcodes\fR
+Reads will only be put in barcode bins if they have
+a strong match for the barcode on both their start
+and end (default: a read can be binned with a match
+at its start or end)
+.TP
+\fB\-\-untrimmed\fR
+Bin reads but do not trim them (appropriate if reads
+are to be used with Nanopolish) (default: trim the
+reads)
+.TP
+\fB\-\-discard_unassigned\fR
+Discard unassigned reads (instead of creating a
+"none" bin) (default: False)
+.SS "Adapter search settings:"
+.IP
+Control how the program determines which adapter sets are present
+.TP
+\fB\-\-adapter_threshold\fR ADAPTER_THRESHOLD
+An adapter set has to have at least this percent
+identity to be labelled as present and trimmed off
+(0 to 100) (default: 90.0)
+.TP
+\fB\-\-check_reads\fR CHECK_READS
+This many reads will be aligned to all possible
+adapters to determine which adapter sets are present
+(default: 10000)
+.TP
+\fB\-\-scoring_scheme\fR SCORING_SCHEME
+Comma\-delimited string of alignment scores: match,
+mismatch, gap open, gap extend (default: 3,\-6,\-5,\-2)
+.SS "End adapter settings:"
+.IP
+Control the trimming of adapters from read ends
+.TP
+\fB\-\-end_size\fR END_SIZE
+The number of base pairs at each end of the read
+which will be searched for adapter sequences
+(default: 150)
+.TP
+\fB\-\-min_trim_size\fR MIN_TRIM_SIZE
+Adapter alignments smaller than this will be ignored
+(default: 4)
+.TP
+\fB\-\-extra_end_trim\fR EXTRA_END_TRIM
+This many additional bases will be removed next to
+adapters found at the ends of reads (default: 2)
+.TP
+\fB\-\-end_threshold\fR END_THRESHOLD
+Adapters at the ends of reads must have at least
+this percent identity to be removed (0 to 100)
+(default: 75.0)
+.SS "Middle adapter settings:"
+.IP
+Control the splitting of read from middle adapters
+.TP
+\fB\-\-no_split\fR
+Skip splitting reads based on middle adapters
+(default: split reads when an adapter is found in
+the middle)
+.TP
+\fB\-\-discard_middle\fR
+Reads with middle adapters will be discarded
+(default: reads with middle adapters are split)
+(this option is on by default when outputting reads
+into barcode bins)
+.TP
+\fB\-\-middle_threshold\fR MIDDLE_THRESHOLD
+Adapters in the middle of reads must have at least
+this percent identity to be found (0 to 100)
+(default: 85.0)
+.TP
+\fB\-\-extra_middle_trim_good_side\fR EXTRA_MIDDLE_TRIM_GOOD_SIDE
+This many additional bases will be removed next to
+middle adapters on their "good" side (default: 10)
+.TP
+\fB\-\-extra_middle_trim_bad_side\fR EXTRA_MIDDLE_TRIM_BAD_SIDE
+This many additional bases will be removed next to
+middle adapters on their "bad" side (default: 100)
+.TP
+\fB\-\-min_split_read_size\fR MIN_SPLIT_READ_SIZE
+Post\-split read pieces smaller than this many base
+pairs will not be outputted (default: 1000)
+.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/rules

@@ -9,10 +9,10 @@ include /usr/share/dpkg/default.mk
 %:
 	dh $@ --with python3
 
-override_dh_install:
-	dh_install
-	mkdir -p debian/$(DEB_SOURCE)/usr/lib/$(DEB_HOST_MULTIARCH)/$(DEB_SOURCE)
-	cp -a porechop/cpp_functions.so debian/$(DEB_SOURCE)/usr/lib/$(DEB_HOST_MULTIARCH)/$(DEB_SOURCE)
-#	for so in `find . -name *.so` ; do \
-#	    cp $${so} debian/$(DEB_SOURCE)/usr/lib/$(DEB_HOST_MULTIARCH)/$(DEB_SOURCE)/`echo $${so} | sed 's/.cpython-[0-9]\+m-$(DEB_HOST_MULTIARCH)//'` ; \
-#	done
+override_dh_python3:
+	dh_python3
+	# for some very strange reason dh_python3 is renaming cpp_functions.so to cpp_functions.cpython-36m-$(DEB_SOURCE).so
+	# Just revert this!
+	mv debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/$(DEB_SOURCE)/cpp_functions*.so debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/$(DEB_SOURCE)/cpp_functions.so
+	# Did everything worked???
+	find . -name "*.so"

debian/tests/run-unit-test

@@ -7,4 +7,4 @@ if [ "$ADTTMP" = "" ] ; then
     trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
 fi
  
-porechop -v
+porechop -h