debian/changelog

-skesa (2.3.0-1) UNRELEASED; urgency=medium
+skesa (2.3.0-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #932294)
 
- -- Andreas Tille <tille@debian.org>  Wed, 17 Jul 2019 10:54:03 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 17 Jul 2019 13:55:35 +0200

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: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+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 --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

+skesa	usr/bin

debian/manpages

+debian/*.1

debian/patches/hardening.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 17 Jul 2019 10:54:03 +0200
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -40,10 +40,10 @@ NGS_INCL := -I $(NGS_PATH)/include
+ NGS_LIB := -L $(NGS_PATH)/lib64
+ 
+ CC = c++ -std=c++11
+-CFLAGS = -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
++CFLAGS += -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
+          -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
+          
+-LIBS = $(VDB_LIB) -lncbi-ngs-c++ -lncbi-vdb \
++LIBS += $(VDB_LIB) -lncbi-ngs-c++ -lncbi-vdb \
+        $(NGS_LIB) -lngs-c++-static \
+        -Wl,-Bstatic $(BOOST_LIB) \
+        -lboost_program_options \
+@@ -63,7 +63,7 @@ glb_align.o: glb_align.hpp Makefile
+ 
+ skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile
+ skesa: skesa.o glb_align.o
+-	$(CC) -o $@ $^ $(LIBS)
++	$(CC) -o $@ $^ $(LIBS) $(LDFLAGS)
+ 
+ $(NGS_DIR)/ngs.done:
+ 	rm -fr $(NGS_DIR)

debian/patches/series

 use_debian_packaged_ngs-sdk.patch
+hardening.patch

debian/skesa.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH SKESA "1" "July 2019" "skesa 2.3.0" "User Commands"
+.SH NAME
+skesa \- strategic Kmer extension for scrupulous assemblies
+.SH DESCRIPTION
+SKESA is a DeBruijn graph-based de-novo assembler designed for
+assembling reads of microbial genomes sequenced using Illumina.
+Comparison with SPAdes and MegaHit shows that SKESA produces assemblies
+that have high sequence quality and contiguity, handles low-level
+contamination in reads, is fast, and produces an identical assembly for
+the same input when assembled multiple times with the same or different
+compute resources. SKESA has been used for assembling over 272,000 read
+sets in the Sequence Read Archive at NCBI and for real-time pathogen
+detection.
+.SH OPTIONS
+.SS "General options:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+Produce help message
+.TP
+\fB\-v\fR [ \fB\-\-version\fR ]
+Print version
+.TP
+\fB\-\-cores\fR arg (=0)
+Number of cores to use (default all) [integer]
+.TP
+\fB\-\-memory\fR arg (=32)
+Memory available (GB, only for sorted counter)
+[integer]
+.TP
+\fB\-\-hash_count\fR
+Use hash counter [flag]
+.TP
+\fB\-\-estimated_kmers\fR arg (=100)
+Estimated number of unique kmers for bloom
+filter (M, only for hash counter) [integer]
+.TP
+\fB\-\-skip_bloom_filter\fR
+Don't do bloom filter; use \fB\-\-estimated_kmers\fR as
+the hash table size (only for hash counter)
+[flag]
+.SS "Input/output options : at least one input providing reads for assembly must be specified:"
+.TP
+\fB\-\-fasta\fR arg
+Input fasta file(s) (could be used multiple
+times for different runs) [string]
+.TP
+\fB\-\-fastq\fR arg
+Input fastq file(s) (could be used multiple
+times for different runs) [string]
+.TP
+\fB\-\-use_paired_ends\fR
+Indicates that a single (not comma separated)
+fasta/fastq file contains paired reads [flag]
+.TP
+\fB\-\-sra_run\fR arg
+Input sra run accession (could be used multiple
+times for different runs) [string]
+.TP
+\fB\-\-contigs_out\fR arg
+Output file for contigs (stdout if not
+specified) [string]
+.SS "Assembly options:"
+.TP
+\fB\-\-kmer\fR arg (=21)
+Minimal kmer length for assembly [integer]
+.TP
+\fB\-\-min_count\fR arg
+Minimal count for kmers retained for comparing
+alternate choices [integer]
+.TP
+\fB\-\-max_kmer_count\fR arg
+Minimum acceptable average count for estimating
+the maximal kmer length in reads [integer]
+.TP
+\fB\-\-vector_percent\fR arg (=0.05)
+Count for  vectors as a fraction of the read
+number (1. disables) [float (0,1]]
+.TP
+\fB\-\-insert_size\fR arg
+Expected insert size for paired reads (if not
+provided, it will be estimated) [integer]
+.TP
+\fB\-\-steps\fR arg (=11)
+Number of assembly iterations from minimal to
+maximal kmer length in reads [integer]
+.TP
+\fB\-\-fraction\fR arg (=0.1)
+Maximum noise to signal ratio acceptable for
+extension [float [0,1)]
+.TP
+\fB\-\-max_snp_len\fR arg (=150)
+Maximal snp length [integer]
+.TP
+\fB\-\-min_contig\fR arg (=200)
+Minimal contig length reported in output
+[integer]
+.TP
+\fB\-\-allow_snps\fR
+Allow additional step for snp discovery [flag]
+.SS "Debugging options:"
+.TP
+\fB\-\-force_single_ends\fR
+Don't use paired\-end information [flag]
+.TP
+\fB\-\-seeds\fR arg
+Input file with seeds [string]
+.TP
+\fB\-\-all\fR arg
+Output fasta for each iteration [string]
+.TP
+\fB\-\-dbg_out\fR arg
+Output kmer file [string]
+.TP
+\fB\-\-hist\fR arg
+File for histogram [string]
+.TP
+\fB\-\-connected_reads\fR arg
+File for connected paired reads [string]
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.