[med-svn] [plast] 02/04: Add initial Debian dir
Andreas Tille
tille at debian.org
Tue Feb 9 17:30:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository plast.
commit 2581cad94e24fe58e6915145ffe97a5a8edc7119
Author: Andreas Tille <tille at debian.org>
Date: Tue Feb 9 14:55:27 2016 +0100
Add initial Debian dir
---
debian/bin/plast | 236 +++++++++++++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 27 ++
debian/copyright | 619 +++++++++++++++++++++++++++++++++
debian/dirs | 2 +
debian/install | 1 +
debian/manpages | 1 +
debian/patches/fix_format_string.patch | 15 +
debian/patches/series | 1 +
debian/plast.1 | 185 ++++++++++
debian/rules | 26 ++
debian/source/format | 1 +
debian/upstream/metadata | 11 +
debian/watch | 4 +
15 files changed, 1135 insertions(+)
diff --git a/debian/bin/plast b/debian/bin/plast
new file mode 100755
index 0000000..29b8193
--- /dev/null
+++ b/debian/bin/plast
@@ -0,0 +1,236 @@
+#!/bin/sh
+# This is an adapted wrapper script from original
+# srcipts/plast.sh
+# by adapting the launch() procedure to /usr/lib/plast/bin/plast
+# For changes make sure you create a diff
+#
+
+#/*****************************************************************************
+# * *
+# * PLAST : Parallel Local Alignment Search Tool *
+# * Copyright (c) 2009-2015 Inria *
+# * *
+# * PLAST is free software; you can redistribute it and/or modify it under *
+# * the Affero GPL v3 License *
+# * *
+# * This program is distributed in the hope that it will be useful, *
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+# * CECILL version 2 License for more details. *
+# *****************************************************************************/
+
+# start plast execution: you can adapt _scripts_dir as needed if you install
+# plast binary elsewhere than build/bin
+launch() {
+ #_scripts_dir=$( cd -P -- "$(dirname -- "$(command -v -- "$0")")" && pwd -P )
+ /usr/lib/plast/bin/plast $KL_PARAMS
+}
+
+choose_query() {
+ breakline
+ echo "Enter the path to your query file (use [tab] key for completion): "
+ read -e -p ">" query
+
+ if [ -z $query ]; then
+ echo "/!\ You did not specify a file."
+ choose_query
+ elif [ -e $query ]; then
+ choose_bank
+ else
+ echo "/!\ Query does not exist."
+ choose_query
+ fi
+}
+
+choose_bank() {
+ breakline
+ echo "What is the type of your reference databank ? "
+ echo "1. FASTA file"
+ echo "2. Blast databank"
+ read -n 1 -p "Your choice: " db_type
+ echo
+
+ case $db_type in
+ 1) choose_bank_fasta ;;
+ 2) choose_bank_blast ;;
+ *) echo "/!\ Invalid choice."
+ choose_bank ;;
+ esac
+}
+
+choose_bank_fasta() {
+ breakline
+ echo "Enter the path to the FASTA file (use [tab] key for completion): "
+ read -e -p ">" bank
+ if [ -z $bank ]; then
+ echo "/!\ You did not specify a file."
+ choose_bank_fasta
+ elif [ -e $bank ]; then
+ choose_program
+ else
+ echo "/!\ Fasta file does not exist."
+ choose_bank_fasta
+ fi
+}
+
+choose_bank_blast() {
+ breakline
+ echo "Enter the path to the Blast databank file (.pin or .pal or .nin or .nal): "
+ read -e -p ">" bank
+ if [ -z $bank ]; then
+ echo "/!\ You did not specify a file."
+ choose_bank_blast
+ elif [ -e $bank ]; then
+ choose_program
+ else
+ echo "/!\ Blast databank file does not exist."
+ choose_bank_blast
+ fi
+}
+
+choose_program() {
+ breakline
+ echo "Choose your sequence comparison method: "
+ echo "1. PLASTp: Scan a protein database with a protein query"
+ echo "2. PLASTn: Scan a nucleic database with a nucleic query"
+ echo "3. PLASTx: Scan a protein database with a translated nucleic query"
+ echo "4. tPLASTn: Scan a translated nucleic database with a protein query"
+ echo "5. tPLASTx: Scan a translated nucleic database with a translated nucleic query"
+ read -n 1 -p "Your choice: " choice
+ echo
+
+ case $choice in
+ 1) program="plastp"
+ choose_mhpq ;;
+ 2) program="plastn"
+ choose_plastn_mode ;;
+ 3) program="plastx"
+ choose_mhpq ;;
+ 4) program="tplastn"
+ choose_mhpq ;;
+ 5) program="tplastx"
+ choose_mhpq ;;
+ *) echo "/!\ Invalid choice."
+ choose_program ;;
+ esac
+}
+
+choose_plastn_mode() {
+ breakline
+ read -p "Are you comparing close homologues ? (y/n) " -n 1 -r
+ echo
+ if [[ $REPLY =~ ^[Yy]$ ]]; then
+ def_evalue='1e-100'
+ specials_args='-s 127 -xdrop-ungap 0 -Z 0 -max-database-size 5000000'
+ fi
+ choose_mhpq
+}
+
+choose_mhpq() {
+ breakline
+ read -p "Maximum hits per query ? Value 0 will dump all hits (10 by default): " mhpq
+ mhpq=${mhpq:-10}
+
+ if echo $mhpq | egrep -q '^[0-9]+$'; then
+ choose_evalue
+ else
+ echo "/!\ Wrong value."
+ choose_mhpq
+ fi
+}
+
+choose_evalue() {
+ breakline
+ read -p "E-value threshold ? (default is $def_evalue): " evalue
+ evalue=${evalue:-$def_evalue}
+
+ if echo $evalue | egrep -q '^[+-]?((([0-9]+(\.[0-9]*)?)|(\.[0-9]+))([eE][+-]?[0-9]+)?)$'; then
+ choose_out
+ else
+ echo "/!\ Wrong value."
+ choose_evalue
+ fi
+}
+
+choose_out() {
+ breakline
+ read -p "PLAST result file name (out.csv by default): " out
+ out=${out:-"out.csv"}
+
+ if [ -e $out ]
+ then
+ read -p "/!\ File already exists. Overwrite it ? (y/n) " -n 1 -r
+ echo
+ if [[ $REPLY =~ ^[Yy]$ ]]; then
+ choose_outfmt
+ else
+ choose_out
+ fi
+ else
+ choose_outfmt
+ fi
+}
+
+choose_outfmt() {
+ breakline
+ echo "Choose result format: "
+ echo "1. tabular Blast-like"
+ echo "2. extended tabular format"
+ echo "3. XML Blast-like"
+ read -n 1 -p "Your choice: " choice
+ echo
+
+ case $choice in
+ 1) out_fmt="1"
+ validate ;;
+ 2) out_fmt="2"
+ validate ;;
+ 3) out_fmt="4"
+ validate ;;
+ *) echo "/!\ Invalid choice."
+ choose_outfmt ;;
+ esac
+}
+
+
+validate() {
+ breakline
+ KL_PARAMS='-p '$program' -i '$query' -d '$bank' -max-hit-per-query '$mhpq' -e '$evalue' -o '$out
+ KL_PARAMS=$KL_PARAMS' -outfmt '$out_fmt' '$specials_args' -force-query-order 1000 -stats '$out'.stats'
+ KL_PARAMS=$KL_PARAMS' -bargraph '
+
+ echo "PLAST arguments are: "$KL_PARAMS
+ echo
+ echo "IMPORTANT: ensure your terminal can display at least 150 chars/line to display PLAST progress bar."
+ echo
+ read -p "Ready to start PLAST ? (y/n) " -n 1 -r
+ echo
+ breakline
+ if [[ $REPLY =~ ^[Yy]$ ]]; then
+ launch
+ elif [[ $REPLY =~ ^[Nn]$ ]]; then
+ helper
+ else
+ validate
+ fi
+}
+
+breakline() {
+ echo
+ echo "_____________________"
+}
+
+helper() {
+ # init default values
+ def_evalue='1e-3'
+ specials_args=''
+
+ choose_query
+}
+
+if [ $# -eq 0 ]; then
+ helper
+else
+ KL_PARAMS=$*
+ launch
+fi
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..1b9e936
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+plast (2.3.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 09 Feb 2016 10:20:36 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..1fbc4c8
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: plast
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cmake,
+ default-jdk
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/plast/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/plast/trunk/
+Homepage: https://plast.inria.fr/
+
+Package: plast
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${java:Depends}
+Description: Parallel Local Sequence Alignment Search Tool
+ PLAST is a fast, accurate and NGS scalable bank-to-bank sequence
+ similarity search tool providing significant accelerations of seeds-
+ based heuristic comparison methods, such as the Blast suite of
+ algorithms.
+ .
+ Relying on unique software architecture, PLAST takes full advantage of
+ recent multi-core personal computers without requiring any additional
+ hardware devices.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..3c13833
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,619 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PLAST
+Source: https://plast.inria.fr/developer-guide/
+Files-Excluded: src/pcre
+
+Files: *
+Copyright: 2009-2015 Van Hoa Nguyen and Dominique Lavenier (Inria)
+License: AGPL-3
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: AGPL-3
+
+License: AGPL-3
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ .
+ Version 3, 19 November 2007
+ .
+ Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+ All other non-permissive additional terms are considered "further restrictions"
+ within the meaning of section 10. If the Program as you received it, or any
+ part of it, contains a notice stating that it is governed by this License along
+ with a term that is a further restriction, you may remove that term. If a
+ license document contains a further restriction but permits relicensing or
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+ 8. Termination.
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+ of parties who have received copies or rights from you under this License. If
+ your rights have been terminated and not permanently reinstated, you do not
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+ .
+ 9. Acceptance Not Required for Having Copies.
+ .
+ You are not required to accept this License in order to receive or run a copy
+ of the Program. Ancillary propagation of a covered work occurring solely as a
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+ Each time you convey a covered work, the recipient automatically receives a
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+ counterclaim in a lawsuit) alleging that any patent claim is infringed by
+ making, using, selling, offering for sale, or importing the Program or any
+ portion of it.
+ .
+ 11. Patents.
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+ A "contributor" is a copyright holder who authorizes use under this License of
+ the Program or a work on which the Program is based. The work thus licensed is
+ called the contributor's "contributor version".
+ .
+ A contributor's "essential patent claims" are all patent claims owned or
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+ entered into that arrangement, or that patent license was granted, prior to 28
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+ .
+ Nothing in this License shall be construed as excluding or limiting any implied
+ license or other defenses to infringement that may otherwise be available to
+ you under applicable patent law.
+ .
+ 12. No Surrender of Others' Freedom.
+ .
+ If conditions are imposed on you (whether by court order, agreement or
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+ you from the conditions of this License. If you cannot convey a covered work so
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+ example, if you agree to terms that obligate you to collect a royalty for
+ further conveying from those to whom you convey the Program, the only way you
+ could satisfy both those terms and this License would be to refrain entirely
+ from conveying the Program.
+ .
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+ .
+ Notwithstanding any other provision of this License, if you modify the Program,
+ your modified version must prominently offer all users interacting with it
+ remotely through a computer network (if your version supports such interaction)
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+ covered by version 3 of the GNU General Public License that is incorporated
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+ .
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+ link or combine any covered work with a work licensed under version 3 of the
+ GNU General Public License into a single combined work, and to convey the
+ resulting work. The terms of this License will continue to apply to the part
+ which is the covered work, but the work with which it is combined will remain
+ governed by version 3 of the GNU General Public License.
+ .
+ 14. Revised Versions of this License.
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+ The Free Software Foundation may publish revised and/or new versions of the GNU
+ Affero General Public License from time to time. Such new versions will be
+ similar in spirit to the present version, but may differ in detail to address
+ new problems or concerns.
+ .
+ Each version is given a distinguishing version number. If the Program specifies
+ that a certain numbered version of the GNU Affero General Public License "or
+ any later version" applies to it, you have the option of following the terms
+ and conditions either of that numbered version or of any later version
+ published by the Free Software Foundation. If the Program does not specify a
+ version number of the GNU Affero General Public License, you may choose any
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+ .
+ If the Program specifies that a proxy can decide which future versions of the
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+ 15. Disclaimer of Warranty.
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+ LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER
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+ QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
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+ .
+ 16. Limitation of Liability.
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+ PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
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+ PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY
+ HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+ .
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+ If the disclaimer of warranty and limitation of liability provided above cannot
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+ liability accompanies a copy of the Program in return for a fee.
+ .
+ END OF TERMS AND CONDITIONS
+ .
+ How to Apply These Terms to Your New Programs
+ .
+ If you develop a new program, and you want it to be of the greatest possible
+ use to the public, the best way to achieve this is to make it free software
+ which everyone can redistribute and change under these terms.
+ .
+ To do so, attach the following notices to the program. It is safest to attach
+ them to the start of each source file to most effectively state the exclusion
+ of warranty; and each file should have at least the "copyright" line and a
+ pointer to where the full notice is found.
+ .
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+ .
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as
+ published by the Free Software Foundation, either version 3 of the
+ License, or (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+ .
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ Also add information on how to contact you by electronic and paper mail.
+ .
+ If your software can interact with users remotely through a computer network,
+ you should also make sure that it provides a way for users to get its source.
+ For example, if your program is a web application, its interface could display
+ a "Source" link that leads users to an archive of the code. There are many ways
+ you could offer source, and different solutions will be better for different
+ programs; see section 13 for the specific requirements.
+ .
+ You should also get your employer (if you work as a programmer) or school, if
+ any, to sign a "copyright disclaimer" for the program, if necessary. For more
+ information on this, and how to apply and follow the GNU AGPL, see <http://
+ www.gnu.org/licenses/>.
diff --git a/debian/dirs b/debian/dirs
new file mode 100644
index 0000000..79a9c06
--- /dev/null
+++ b/debian/dirs
@@ -0,0 +1,2 @@
+usr/bin
+usr/lib/plast/bin
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..8e71dae
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+debian/bin usr
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/fix_format_string.patch b/debian/patches/fix_format_string.patch
new file mode 100644
index 0000000..a183566
--- /dev/null
+++ b/debian/patches/fix_format_string.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 09 Feb 2016 10:20:36 +0100
+Description: Fix for more picky gcc-5
+
+--- a/src/tools/PlastCmd.cpp
++++ b/src/tools/PlastCmd.cpp
+@@ -159,7 +159,7 @@ int main (int argc, char* argv[])
+ }
+ catch (...)
+ {
+- fprintf (stderr, MSG_MAIN_MSG4);
++ fprintf (stderr, "%s", MSG_MAIN_MSG4);
+ }
+
+ return 0;
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..bfe0e35
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_format_string.patch
diff --git a/debian/plast.1 b/debian/plast.1
new file mode 100644
index 0000000..60123ee
--- /dev/null
+++ b/debian/plast.1
@@ -0,0 +1,185 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH PLAST "1" "February 2016" "plast 2.3.1" "User Commands"
+.SH NAME
+plast \- Parallel Local Sequence Alignment Search Tool
+.SH DESCRIPTION
+plast 2.3.1
+.IP
+\- Build date: 2016\-02\-09 09:47:45
+\- OS: Linux\-4.3.0\-1\-amd64
+\- Compiler: \fI\,/usr/bin/cc\/\fP (5.3.1)
+\- Host CPU: 4 cores available
+.PP
+[*] denotes mandatory argument.
+.TP
+\fB\-p\fR [*]:
+Program Name [plastp, tplastn, plastx, tplastx or plastn]
+.TP
+\fB\-d\fR [*]:
+Subject database file
+.TP
+\fB\-i\fR [*]:
+Query database file
+.TP
+\fB\-o\fR :
+PLAST report Output File
+.TP
+\fB\-e\fR :
+Expectation value
+.TP
+\fB\-n\fR :
+Size of neighbourhood peforming ungapped extension
+.TP
+\fB\-s\fR :
+Ungapped threshold trigger a small gapped extension
+.TP
+\fB\-g\fR :
+threshold for small gapped extension
+.TP
+\fB\-b\fR :
+bandwith for small gapped extension
+.TP
+\fB\-a\fR :
+Number of processors to use
+.TP
+\fB\-G\fR :
+Cost to open a gap
+.TP
+\fB\-E\fR :
+Cost to extend a gap
+.TP
+\fB\-xdrop\-ungap\fR :
+X dropoff value for Ungapped alignment (in bits) (zero invokes default behavior 20 bits)
+.TP
+\fB\-X\fR :
+X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
+.TP
+\fB\-Z\fR :
+X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
+.TP
+\fB\-index\-threshold\fR :
+Index threshold to calculate the similarity between neighbour
+.TP
+\fB\-F\fR :
+Filter query sequence
+.TP
+\fB\-M\fR :
+Score matrix (BLOSUM62 or BLOSUM50)
+.TP
+\fB\-strand\fR :
+strands for plastn: 'plus', 'minus' or 'both' (default)
+.TP
+\fB\-r\fR :
+reward for a nucleotide match (plastn)
+.TP
+\fB\-q\fR :
+penalty for a nucleotide mismatch (plastn)
+.TP
+\fB\-force\-query\-order\fR :
+Force queries ordering in output file.
+.TP
+\fB\-max\-database\-size\fR :
+Maximum allowed size (in bytes) for a database. If greater, database is segmented.
+.TP
+\fB\-max\-hit\-per\-query\fR :
+Maximum hits per query. 0 value will dump all hits (default)
+.TP
+\fB\-max\-hsp\-per\-hit\fR :
+Maximum alignments per hit. 0 value will dump all hits (default)
+.TP
+\fB\-outfmt\fR :
+Output format: 1 for tabulated (default), 2 for extended tubulated, 4 for NCBI Blast\-like.
+.TP
+\fB\-strands\-list\fR :
+List of the strands (ex: "1,2,6") to be used when using algo using nucleotids databases.
+.TP
+\fB\-optim\-codon\-stop\fR :
+size of the allowed range between the last invalid character and the next stop codon
+.TP
+\fB\-factory\-dispatcher\fR :
+Factory that creates dispatcher.
+.TP
+\fB\-factory\-statistics\fR :
+Factory that creates statistics builder.
+.TP
+\fB\-factory\-indexation\fR :
+Factory that creates indexation builder.
+.TP
+\fB\-factory\-hit\-ungap\fR :
+Factory that creates ungap hits iterator.
+.TP
+\fB\-factory\-hit\-smallgap\fR :
+Factory that creates small gap hits iterator.
+.TP
+\fB\-factory\-hit\-fullgap\fR :
+Factory that creates full gap hits iterator.
+.TP
+\fB\-factory\-hit\-composition\fR :
+Factory that creates composition hits iterator.
+.TP
+\fB\-factory\-gap\-result\fR :
+Factory that creates gap alignments result.
+.TP
+\fB\-factory\-ungap\-result\fR :
+Factory that creates ungap alignments result.
+.TP
+\fB\-splitter\fR :
+Factory that creates an alignment splitter. String: 'normal' or 'banded' (default)
+.TP
+\fB\-optim\-filter\-ungap\fR :
+Optimization that filters out through ungap alignments.
+.TP
+\fB\-bargraph\fR :
+Display a progress bar during execution.
+.TP
+\fB\-bargraph\-size\fR :
+Nb of characters of the bargraph.
+.TP
+\fB\-progression\-file\fR :
+Dump in a file the current execution percentage.
+.TP
+\fB\-verbose\fR :
+Display information during algorithm execution.
+.TP
+\fB\-full\-stats\fR :
+Dump algorithm statistics.
+.TP
+\fB\-stats\fR :
+Dump generic statistics.
+.TP
+\fB\-stats\-fmt\fR :
+Format of statistics: 'raw' (default) or 'xml'
+.TP
+\fB\-stats\-auto\fR :
+Automatic stats file creation
+.TP
+\fB\-alignment\-progress\fR :
+Dump in a file the growing number of ungap/ungap alignments during algorithm.
+.TP
+\fB\-resources\-progress\fR :
+Dump in a file information about resources during algorithm.
+.TP
+\fB\-plastrc\fR :
+Pathname of the plast config file.
+.TP
+\fB\-xmlfilter\fR :
+Uri of a XML filter file.
+.TP
+\fB\-seeds\-use\-ratio\fR :
+Ratio of seeds to be used.
+.TP
+\fB\-seeds\-index\-filter\fR :
+seeds length to be used for the indexation filter.
+.TP
+\fB\-complete\-subject\-database\-stats\-file\fR :
+File path to the stats of the complete subject database
+.TP
+\fB\-W\fR :
+size of the seeds
+.TP
+\fB\-h\fR :
+help
+.PP
+Citing PLAST: Nguyen VH, Lavenier D. (2009) PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, vol 10, no 329.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..fdcee94
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@ --buildsystem=cmake
+
+override_dh_install:
+ dh_install
+ # install binary
+ cp -a */bin/*/plast debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/bin
+ # no need for the includes
+ rm -rf debian/*/usr/include
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..6d058a9
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Van Hoa Nguyen and Dominique Lavenier
+ Title: "PLAST: parallel local alignment search tool for database comparison"
+ Journal: BMC Bioinformatics
+ Year: 2009
+ Volume: 10
+ Pages: 329
+ DOI: 10.1186/1471-2105-10-329
+ PMID: 19821978
+ URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-329
+ eprint: http://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-329?site=bmcbioinformatics.biomedcentral.com
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..bda7dca
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://plast.inria.fr/developer-guide/ .*/files/plast_source_v(\d[\d.]+)\.tar\.gz
--
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