debian/changelog

@@ -9,6 +9,7 @@ discosnp (2.3.0-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/control
   * Remove trailing whitespace in debian/copyright
   * Build-Depends: libboost-dev, libgatbcore-dev, libhdf5-dev, zlib1g-dev
+  * Fix dh_install
 
  -- Andreas Tille <tille@debian.org>  Sat, 20 Oct 2018 10:56:58 +0200
 

debian/control

@@ -20,6 +20,8 @@ Architecture: any
 Depends: ${misc:Depends},
          ${shlibs:Depends},
          ${python3:Depends}
+         python3
+Recommends: gatb-core
 Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads
  Software discoSnp is designed for discovering Single Nucleotide
  Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation

debian/copyright

@@ -6,20 +6,11 @@ Files: *
 Copyright: 2013 INRIA / IRISA
 License: CeCILL
 
-Files: minia/*
-Copyright: 2012 Rayan Chiki <rayan.chikhi@ens-cachan.org>
-           2012 Guillaume Rizk
-License: CeCILL
-
-Files: kissreads/include/libchash.h
+Files: tools/kissreads2/src/libchash.h
 Copyright: 1998-2005, Google Inc
            1998-2005 Craig Silverstein
 License: BSD-3-clause
 
-Files: minia/ttmath/*
-Copyright: Tomasz Sowa <t.sowa@ttmath.org>
-License: BSD-3-clause
-
 Files: debian/*
 Copyright: 2013 Olivier Sallou <osallou@debian.org>
 License: GPLv-2

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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=kissnp2
+help2man --no-info --no-discard-stderr --help-option=" -help" \
+         --name="detects SNPs and indels from read sets" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=kissreads2
+help2man --no-info --no-discard-stderr --help-option=" -help" \
+         --name="enhances the kissnp2 results by computing per read set" \
+            --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/discosnp.install

-output_analyses/discoSnp_to_csv usr/bin/
-output_analyses/discoSnp_to_genotypes  usr/bin/
-kissnp2/kissnp2 usr/bin/
-kissreads/kissreads usr/bin/
-data_sample usr/share/doc/discosnp/examples/

debian/discosnp.manpages

-kissnp2.1
-kissreads.1

debian/docs

-README.txt
+README*
+doc/*
+test

debian/install

+scripts			usr/share/discosnp
+scripts_RAD		usr/share/discosnp
+run_discoSnp*.sh	usr/bin

debian/kissnp2.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH KISSNP2 "1" "January 2019" "kissnp2 2.3.0" "User Commands"
+.SH NAME
+kissnp2 \- detects SNPs and indels from read sets
+.SH DESCRIPTION
+[Kissnp2 options]
+.TP
+\fB\-x\fR
+(0 arg) :    keep truncated bubbles, that have no successors on the 2 paths at the same position
+.TP
+\fB\-P\fR
+(1 arg) :    maximal number of polymorphism per bubble  [default '1']
+.TP
+\fB\-D\fR
+(1 arg) :    maximal size of a predicted indel  [default '0']
+.TP
+\fB\-dont_output_first_coverage\fR (0 arg) :
+Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants
+.TP
+\fB\-in\fR
+(1 arg) :    input file (likely a hdf5 file)
+.TP
+\fB\-coverage_file\fR
+(1 arg) :    File (.h5) generated by kissnp2, containing the coverage threshold per read set  [default '_removemeplease']
+.TP
+\fB\-out\fR
+(1 arg) :    output name
+.TP
+\fB\-T\fR
+(0 arg) :    extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with \fB\-t\fR
+.TP
+\fB\-t\fR
+(0 arg) :    extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with \fB\-T\fR
+.TP
+\fB\-max_symmetrical_crossroads\fR (1 arg) :
+In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit  [default '\-1']
+.TP
+\fB\-b\fR
+(1 arg) :    branching mode
+.IP
+0: forbid SNPs for which any of the two paths is branching (high precision, low recall)
+1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)
+2: No limitation on branching (low precision, high recall)  [default '1']
+.TP
+\fB\-max_ambigous_indel\fR
+(1 arg) :    Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output  [default '20']
+.TP
+\fB\-l\fR
+(0 arg) :    conserve low complexity SNPs
+.TP
+\fB\-nb\-cores\fR
+(1 arg) :    number of cores  [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) :    verbosity level  [default '1']
+.TP
+\fB\-version\fR
+(0 arg) :    version
+.TP
+\fB\-help\fR
+(0 arg) :    help
+.TP
+\fB\-bfs\-max\-depth\fR
+(1 arg) :    maximum depth for BFS  [default '200']
+.TP
+\fB\-bfs\-max\-breadth\fR
+(1 arg) :    maximum breadth for BFS  [default '20']
+.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/kissreads2.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH KISSREADS2 "1" "January 2019" "kissreads2 2.3.0" "User Commands"
+.SH NAME
+kissreads2 \- enhances the kissnp2 results by computing per read set
+.SH DESCRIPTION
+[Kissreads2 options]
+.TP
+\fB\-x\fR
+(0 arg) :    radseq option, homogeneous read depth along the prediction
+.TP
+\fB\-predictions\fR
+(1 arg) :    Input predictions
+.TP
+\fB\-reads\fR
+(1 arg) :    Input reads
+.TP
+\fB\-unco\fR
+(1 arg) :    Output uncoherent file name  [default '/dev/null']
+.TP
+\fB\-co\fR
+(1 arg) :    Output coherent file name
+.TP
+\fB\-hamming\fR
+(1 arg) :    Maximal hamming distance authorized while maping  [default '1']
+.TP
+\fB\-coverage_file\fR (1 arg) :
+File (.h5) generated by kissnp2, containing the coverage threshold per read set  [default '_removemeplease']
+.TP
+\fB\-k\fR
+(1 arg) :    Size of k, used as minial overlap and kmer spanning read coherence  [default '31']
+.TP
+\fB\-index_stride\fR
+(1 arg) :    Index Stride  [default '2']
+.TP
+\fB\-size_seeds\fR
+(1 arg) :    Size of the used seeds (distinct from the size of k)  [default '25']
+.TP
+\fB\-output_fasta\fR
+(0 arg) :    Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline
+.TP
+\fB\-genotype\fR
+(0 arg) :    Compute genotypes
+.TP
+\fB\-nb\-cores\fR
+(1 arg) :    number of cores  [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) :    verbosity level  [default '1']
+.TP
+\fB\-version\fR
+(0 arg) :    version
+.TP
+\fB\-help\fR
+(0 arg) :    help
+.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/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

debian/manpages

+debian/*.1

debian/patches/no_install_to_wrong_dir.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Failed to fix these install dirs, deactivate completely and use dh_install
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -81,12 +81,12 @@ SET (CPACK_SOURCE_IGNORE_FILES
+ )
+ 
+ # For creating the BINARY package we include the files we want
+-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc                DESTINATION .)
+-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test               DESTINATION .)
+-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts            DESTINATION . FILES_MATCHING REGEX ".*\\.(py|sh)$"  PATTERN "jenkins" EXCLUDE)
+-INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/run_discoSnp++.sh  DESTINATION .)
+-INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/README.md          DESTINATION .)
+-INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE            DESTINATION .)
++#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc                DESTINATION .)
++#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test               DESTINATION .)
++#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts            DESTINATION . FILES_MATCHING REGEX ".*\\.(py|sh)$"  PATTERN "jenkins" EXCLUDE)
++#INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/run_discoSnp++.sh  DESTINATION .)
++#INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/README.md          DESTINATION .)
++#INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE            DESTINATION .)
+ 
+ # We include the "bin" tag into binary archive file name
+ set (CPACK_PACKAGE_FILE_NAME  ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})

debian/patches/path_to_readme_file_names.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: There is no point in delivering read_file_names in /usr/bin
+ It is available in /usr/share/discosnp/bin/read_file_names - this patch adapts
+ the scripts using it.
+ .
+ Some other issues of these scripts are fixed as well.
+
+--- a/run_discoSnpRad.sh
++++ b/run_discoSnpRad.sh
+@@ -65,7 +65,7 @@ genotyping="-genotype"
+ remove=1
+ verbose=1
+ short_read_connector_path=""
+-EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
++EDIR=/usr
+ 
+ if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
+     read_file_names_bin=$EDIR/build/bin/read_file_names
+@@ -73,14 +73,14 @@ if [ -d "$EDIR/build/" ] ; then # VERSIO
+     kissnp2_bin=$EDIR/build/bin/kissnp2
+     kissreads2_bin=$EDIR/build/bin/kissreads2
+ else # VERSION BINARY
+-    read_file_names_bin=$EDIR/bin/read_file_names
++    read_file_names_bin=/usr/lib/discosnp/bin/read_file_names
+     dbgh5_bin=$EDIR/bin/dbgh5
+     kissnp2_bin=$EDIR/bin/kissnp2
+     kissreads2_bin=$EDIR/bin/kissreads2
+ fi
+ 
+ 
+-chmod +x $EDIR/scripts/*.sh $EDIR/scripts_RAD/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
++# chmod +x $EDIR/scripts/*.sh $EDIR/scripts_RAD/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
+ 
+ useref=""
+ genome=""
+--- a/run_discoSnp++.sh
++++ b/run_discoSnp++.sh
+@@ -54,7 +54,7 @@ paired=""
+ remove=1
+ verbose=1
+ e=""
+-EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
++EDIR=/usr
+ 
+ if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
+     read_file_names_bin=$EDIR/build/bin/read_file_names
+@@ -62,13 +62,13 @@ if [ -d "$EDIR/build/" ] ; then # VERSIO
+     kissnp2_bin=$EDIR/build/bin/kissnp2
+     kissreads2_bin=$EDIR/build/bin/kissreads2
+ else # VERSION BINARY
+-    read_file_names_bin=$EDIR/bin/read_file_names
++    read_file_names_bin=/usr/lib/discosnp/bin/read_file_names
+     dbgh5_bin=$EDIR/bin/dbgh5
+     kissnp2_bin=$EDIR/bin/kissnp2
+     kissreads2_bin=$EDIR/bin/kissreads2
+ fi
+ 
+-chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
++#chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
+ 
+ useref=""
+ genome=""
+--- a/scripts_RAD/discoRAD_finalization.sh
++++ b/scripts_RAD/discoRAD_finalization.sh
+@@ -61,7 +61,7 @@ cmd="${short_read_connector_directory}/s
+ echo -e "\t\t$cmd"
+ $cmd
+ # Compute the clustering
+-cmd="${EDIR}/../build/bin/quick_hierarchical_clustering ${discofile}.txt > ${discofile}.cluster"
++cmd="/usr/lib/discosnp/bin/quick_hierarchical_clustering ${discofile}.txt > ${discofile}.cluster"
+ echo -e "\t\t$cmd"
+ $cmd  > ${discofile}.cluster
+ # Generate a .fa file with clustering information

debian/patches/series

 use_debian_packaged_gatb-core.patch
+no_install_to_wrong_dir.patch
+path_to_readme_file_names.patch
+spelling.patch

debian/patches/spelling.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Fix spelling
+
+--- a/tools/kissnp2/src/Kissnp2.cpp
++++ b/tools/kissnp2/src/Kissnp2.cpp
+@@ -53,8 +53,8 @@ Kissnp2::Kissnp2 () : Tool ("Kissnp2")
+     getParser()->push_front (new OptionNoParam  (STR_DISCOSNP_LOW_COMPLEXITY,       "conserve low complexity SNPs",     false));
+     getParser()->push_front (new OptionOneParam (STR_MAX_AMBIGOUS_INDELS,           "Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output", false, "20"));
+     getParser()->push_front (new OptionOneParam (STR_DISCOSNP_AUTHORISED_BRANCHING, "branching mode\n"
+-                                                 "\t\t0: forbid SNPs for wich any of the two paths is branching (high precision, low recall)\n"
+-                                                 "\t\t1: forbid SNPs for wich the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)\n"
++                                                 "\t\t0: forbid SNPs for which any of the two paths is branching (high precision, low recall)\n"
++                                                 "\t\t1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)\n"
+                                                  "\t\t2: No limitation on branching (low precision, high recall)",  false, "1"));
+     getParser()->push_front (new OptionOneParam (STR_MAX_SYMMETRICAL_CROSSROADS,"In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit", false, "-1"));
+ 
+@@ -63,7 +63,7 @@ Kissnp2::Kissnp2 () : Tool ("Kissnp2")
+     getParser()->push_front (new OptionOneParam (STR_URI_OUTPUT,                    "output name",                      true));
+     getParser()->push_front (new OptionOneParam (STR_KISSNP2_COVERAGE_FILE_NAME,    "File (.h5) generated by kissnp2, containing the coverage threshold per read set",                      false, "_removemeplease"));
+     getParser()->push_front (new OptionOneParam (STR_URI_INPUT,                     "input file (likely a hdf5 file)",  true));
+-    getParser()->push_front (new OptionNoParam (STR_KISSNP2_DONT_OUTPUT_FIRST_COV, "Don't output the first coverage threshold. Use this option whent the refernece file is used for finding the variants",  false));
++    getParser()->push_front (new OptionNoParam (STR_KISSNP2_DONT_OUTPUT_FIRST_COV, "Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants",  false));
+     
+     
+     getParser()->push_front (new OptionOneParam (STR_MAX_INDEL_SIZE,                "maximal size of a predicted indel", false, "0"));
+--- a/tools/kissreads2/src/Kissreads2.cpp
++++ b/tools/kissreads2/src/Kissreads2.cpp
+@@ -41,7 +41,7 @@ Kissreads2::Kissreads2 () : Tool ("Kissr
+     /** We add options known by kissnp2. */
+     
+     getParser()->push_front (new OptionNoParam (STR_KISSREADS_GENOTYPE,             "Compute genotypes", false));
+-    getParser()->push_front (new OptionNoParam (STR_KISSREADS_OUTPUT_FASTA,         "Output standart Fasta. By default the output is formatted especially for the discoSnp++ pipeline", false));
++    getParser()->push_front (new OptionNoParam (STR_KISSREADS_OUTPUT_FASTA,         "Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline", false));
+     
+     getParser()->push_front (new OptionOneParam (STR_KISSREADS_SIZE_SEEDS,          "Size of the used seeds (distinct from the size of k)",  false, "25"));
+     getParser()->push_front (new OptionOneParam (STR_KISSREADS_INDEX_STRIDE,        "Index Stride", false, "2"));

debian/rules

@@ -5,9 +5,15 @@
 
 include /usr/share/dpkg/default.mk
 
+
 %:
 	dh $@
-	dh_clean
 
-override_dh_auto_configure:
-	dh_auto_configure -- -DLINK_DIRECTORIES:STRING='/usr/$(DEB_HOST_MULTIARCH)/hdf5/serial' # --trace-expand
+override_dh_install:
+	dh_install
+	mkdir -p debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
+	mv debian/$(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
+	for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*python' debian/*/usr/*` ; do \
+	    sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \
+	done