[med-svn] [kraken] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Wed Sep 9 11:42:09 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository kraken.
commit cc5087dc7407aca115362173c63b35feedc61794
Author: Andreas Tille <tille at debian.org>
Date: Wed Sep 9 13:41:37 2015 +0200
Add initial packaging
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 31 +++++++++++++
debian/copyright | 26 +++++++++++
debian/createmanpages | 36 ++++++++++++++++
debian/dirs | 2 +
debian/doc-base | 24 +++++++++++
debian/install | 3 ++
debian/links | 1 +
debian/manpages | 1 +
debian/mans/kraken-build.1 | 86 +++++++++++++++++++++++++++++++++++++
debian/mans/kraken-filter.1 | 9 ++++
debian/mans/kraken-mpa-report.1 | 22 ++++++++++
debian/mans/kraken-report.1 | 9 ++++
debian/mans/kraken-translate.1 | 9 ++++
debian/mans/kraken.1 | 66 ++++++++++++++++++++++++++++
debian/patches/kraken_tmp_dir.patch | 44 +++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 31 +++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++
debian/watch | 7 +++
22 files changed, 427 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f7007dc
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+kraken (0.10.5~beta-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Wed, 09 Sep 2015 11:14:16 +0200
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..3ea37b9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: kraken
+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)
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kraken.git
+Vcs-Git: git://anonscm.debian.org/debian-med/kraken.git
+Homepage: http://ccb.jhu.edu/software/kraken/
+
+Package: kraken
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: assigning taxonomic labels to short DNA sequences
+ Kraken is a system for assigning taxonomic labels to short DNA
+ sequences, usually obtained through metagenomic studies. Previous
+ attempts by other bioinformatics software to accomplish this task have
+ often used sequence alignment or machine learning techniques that were
+ quite slow, leading to the development of less sensitive but much faster
+ abundance estimation programs. Kraken aims to achieve high sensitivity
+ and high speed by utilizing exact alignments of k-mers and a novel
+ classification algorithm.
+ .
+ In its fastest mode of operation, for a simulated metagenome of 100 bp
+ reads, Kraken processed over 4 million reads per minute on a single
+ core, over 900 times faster than Megablast and over 11 times faster than
+ the abundance estimation program MetaPhlAn. Kraken's accuracy is
+ comparable with Megablast, with slightly lower sensitivity and very high
+ precision.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5fc9d14
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: kraken
+Upstream-Contact: Derrick Wood <dwood at cs.jhu.edu>
+Source: https://github.com/DerrickWood/kraken
+
+Files: *
+Copyright: 2013-2015 Derrick Wood <dwood at cs.jhu.edu>
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU 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 General Public License for more details.
+ .
+ On Debian systems you can find a copy of the full text of the GNU General
+ Public License at /usr/share/common-licenses/GPL.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..37c8565
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,36 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+ --name='assigning taxonomic labels to short DNA sequences' \
+ --version-string="$VERSION" kraken > $MANDIR/kraken.1
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+ --name='assigning taxonomic labels to short DNA sequences' \
+ --version-string="$VERSION" kraken-build > $MANDIR/kraken-build.1
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+ --name='assigning taxonomic labels to short DNA sequences' \
+ --version-string="$VERSION" kraken-filter > $MANDIR/kraken-filter.1
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+ --name='assigning taxonomic labels to short DNA sequences' \
+ --version-string="$VERSION" kraken-mpa-report > $MANDIR/kraken-mpa-report.1
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+ --name='assigning taxonomic labels to short DNA sequences' \
+ --version-string="$VERSION" kraken-report > $MANDIR/kraken-report.1
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+ --name='assigning taxonomic labels to short DNA sequences' \
+ --version-string="$VERSION" kraken-translate > $MANDIR/kraken-translate.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/dirs b/debian/dirs
new file mode 100644
index 0000000..cb3b91f
--- /dev/null
+++ b/debian/dirs
@@ -0,0 +1,2 @@
+usr/bin
+usr/lib/kraken
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..ae816e9
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,24 @@
+Document: kraken
+Title: Kraken taxonomic sequence classification system - Operating Manual
+Author: Derrick Wood <dwood at cs.jhu.edu>
+Abstract: assigning taxonomic labels to short DNA sequences
+ Kraken is a system for assigning taxonomic labels to short DNA
+ sequences, usually obtained through metagenomic studies. Previous
+ attempts by other bioinformatics software to accomplish this task have
+ often used sequence alignment or machine learning techniques that were
+ quite slow, leading to the development of less sensitive but much faster
+ abundance estimation programs. Kraken aims to achieve high sensitivity
+ and high speed by utilizing exact alignments of k-mers and a novel
+ classification algorithm.
+ .
+ In its fastest mode of operation, for a simulated metagenome of 100 bp
+ reads, Kraken processed over 4 million reads per minute on a single
+ core, over 900 times faster than Megablast and over 11 times faster than
+ the abundance estimation program MetaPhlAn. Kraken's accuracy is
+ comparable with Megablast, with slightly lower sensitivity and very high
+ precision.
+Section: Science/Biology
+
+Format: html
+Index: /usr/share/doc/kraken/html/index.html
+Files: /usr/share/doc/kraken/html/MANUAL.html
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..9e508bb
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,3 @@
+docs/*.html usr/share/doc/kraken/html
+docs/*.png usr/share/doc/kraken/html
+docs/*.css usr/share/doc/kraken/html
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..d5baa09
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+usr/share/doc/kraken/html/MANUAL.html usr/share/doc/kraken/html/index.html
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/kraken-build.1 b/debian/mans/kraken-build.1
new file mode 100644
index 0000000..8f80a34
--- /dev/null
+++ b/debian/mans/kraken-build.1
@@ -0,0 +1,86 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH KRAKEN-BUILD "1" "September 2015" "kraken-build 0.10.5~beta" "User Commands"
+.SH NAME
+kraken-build \- assigning taxonomic labels to short DNA sequences
+.SH SYNOPSIS
+.B kraken-build
+[\fI\,task option\/\fR] [\fI\,options\/\fR]
+.SH DESCRIPTION
+.SS "Task options (exactly one must be selected):"
+.TP
+\fB\-\-download\-taxonomy\fR
+Download NCBI taxonomic information
+.TP
+\fB\-\-download\-library\fR TYPE
+Download partial library
+(TYPE = one of "bacteria", "plasmids",
+"viruses", "human")
+.TP
+\fB\-\-add\-to\-library\fR FILE
+Add FILE to library
+.TP
+\fB\-\-build\fR
+Create DB from library
+(requires taxonomy d/l'ed and at least one file
+in library)
+.TP
+\fB\-\-rebuild\fR
+Create DB from library like \fB\-\-build\fR, but remove
+existing non\-library/taxonomy files before build
+.TP
+\fB\-\-clean\fR
+Remove unneeded files from a built database
+.TP
+\fB\-\-shrink\fR NEW_CT
+Shrink an existing DB to have only NEW_CT k\-mers
+.TP
+\fB\-\-standard\fR
+Download and create default database
+.TP
+\fB\-\-upgrade\fR
+Upgrade an existing older database to use scrambled
+minimizer ordering (see README for details)
+.TP
+\fB\-\-help\fR
+Print this message
+.TP
+\fB\-\-version\fR
+Print version information
+.SH OPTIONS
+.TP
+\fB\-\-db\fR NAME
+Kraken DB/library name (mandatory except for
+\fB\-\-help\fR/\-\-version)
+.TP
+\fB\-\-threads\fR #
+Number of threads (def: 1)
+.TP
+\fB\-\-new\-db\fR NAME
+New Kraken DB name (shrink task only; mandatory
+for shrink task)
+.TP
+\fB\-\-kmer\-len\fR NUM
+K\-mer length in bp (build/shrink tasks only;
+def: 31)
+.TP
+\fB\-\-minimizer\-len\fR NUM
+Minimizer length in bp (build/shrink tasks only;
+def: 15)
+.TP
+\fB\-\-jellyfish\-hash\-size\fR STR
+Pass a specific hash size argument to jellyfish
+when building database (build task only)
+.TP
+\fB\-\-max\-db\-size\fR SIZE
+Shrink the DB before full build, making sure
+database and index together use <= SIZE gigabytes
+(build task only)
+.TP
+\fB\-\-shrink\-block\-offset\fR NUM
+When shrinking, select the k\-mer that is NUM
+positions from the end of a block of k\-mers
+(default: 1)
+.TP
+\fB\-\-work\-on\-disk\fR
+Perform most operations on disk rather than in
+RAM (will slow down build in most cases)
diff --git a/debian/mans/kraken-filter.1 b/debian/mans/kraken-filter.1
new file mode 100644
index 0000000..917cb80
--- /dev/null
+++ b/debian/mans/kraken-filter.1
@@ -0,0 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH KRAKEN-FILTER "1" "September 2015" "kraken-filter 0.10.5~beta" "User Commands"
+.SH NAME
+kraken-filter \- assigning taxonomic labels to short DNA sequences
+.SH SYNOPSIS
+.B kraken-filter
+[\fI\,--db KRAKEN_DB_NAME\/\fR] [\fI\,--threshold NUM\/\fR] \fI\,<kraken output file(s)>\/\fR
+.SH DESCRIPTION
+
diff --git a/debian/mans/kraken-mpa-report.1 b/debian/mans/kraken-mpa-report.1
new file mode 100644
index 0000000..963f0b3
--- /dev/null
+++ b/debian/mans/kraken-mpa-report.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH KRAKEN-MPA-REPORT "1" "September 2015" "kraken-mpa-report 0.10.5~beta" "User Commands"
+.SH NAME
+kraken-mpa-report \- assigning taxonomic labels to short DNA sequences
+.SH SYNOPSIS
+.B kraken-mpa-report
+[\fI\,--db KRAKEN_DB_NAME\/\fR] [\fI\,options\/\fR] \fI\,<kraken output file(s)>\/\fR
+.SH OPTIONS
+.TP
+\fB\-\-db\fR NAME
+Name of Kraken database
+(default: none)
+.TP
+\fB\-\-show\-zeros\fR
+Display taxa even if they lack a read in any sample
+.TP
+\fB\-\-header\-line\fR
+Display a header line indicating sample IDs
+(sample IDs are the filenames)
+.TP
+\fB\-\-intermediate\-ranks\fR
+Display taxa not at the standard ranks with x__ prefix
diff --git a/debian/mans/kraken-report.1 b/debian/mans/kraken-report.1
new file mode 100644
index 0000000..627372b
--- /dev/null
+++ b/debian/mans/kraken-report.1
@@ -0,0 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH KRAKEN-REPORT "1" "September 2015" "kraken-report 0.10.5~beta" "User Commands"
+.SH NAME
+kraken-report \- assigning taxonomic labels to short DNA sequences
+.SH SYNOPSIS
+.B kraken-report
+[\fI\,--db KRAKEN_DB_NAME\/\fR] [\fI\,--show-zeros\/\fR] \fI\,<kraken output file(s)>\/\fR
+.SH DESCRIPTION
+
diff --git a/debian/mans/kraken-translate.1 b/debian/mans/kraken-translate.1
new file mode 100644
index 0000000..7bc3cc5
--- /dev/null
+++ b/debian/mans/kraken-translate.1
@@ -0,0 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH KRAKEN-TRANSLATE "1" "September 2015" "kraken-translate 0.10.5~beta" "User Commands"
+.SH NAME
+kraken-translate \- assigning taxonomic labels to short DNA sequences
+.SH SYNOPSIS
+.B kraken-translate
+[\fI\,--db KRAKEN_DB_NAME\/\fR] [\fI\,--mpa-format\/\fR] \fI\,<kraken output file(s)>\/\fR
+.SH DESCRIPTION
+
diff --git a/debian/mans/kraken.1 b/debian/mans/kraken.1
new file mode 100644
index 0000000..d369146
--- /dev/null
+++ b/debian/mans/kraken.1
@@ -0,0 +1,66 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH KRAKEN "1" "September 2015" "kraken 0.10.5~beta" "User Commands"
+.SH NAME
+kraken \- assigning taxonomic labels to short DNA sequences
+.SH SYNOPSIS
+.B kraken
+[\fI\,options\/\fR] \fI\,<filename(s)>\/\fR
+.SH OPTIONS
+.TP
+\fB\-\-db\fR NAME
+Name for Kraken DB
+(default: none)
+.TP
+\fB\-\-threads\fR NUM
+Number of threads (default: 1)
+.TP
+\fB\-\-fasta\-input\fR
+Input is FASTA format
+.TP
+\fB\-\-fastq\-input\fR
+Input is FASTQ format
+.TP
+\fB\-\-gzip\-compressed\fR
+Input is gzip compressed
+.TP
+\fB\-\-bzip2\-compressed\fR
+Input is bzip2 compressed
+.TP
+\fB\-\-quick\fR
+Quick operation (use first hit or hits)
+.TP
+\fB\-\-min\-hits\fR NUM
+In quick op., number of hits req'd for classification
+NOTE: this is ignored if \fB\-\-quick\fR is not specified
+.TP
+\fB\-\-unclassified\-out\fR FILENAME
+Print unclassified sequences to filename
+.TP
+\fB\-\-classified\-out\fR FILENAME
+Print classified sequences to filename
+.TP
+\fB\-\-output\fR FILENAME
+Print output to filename (default: stdout); "\-" will
+suppress normal output
+.TP
+\fB\-\-only\-classified\-output\fR
+Print no Kraken output for unclassified sequences
+.TP
+\fB\-\-preload\fR
+Loads DB into memory before classification
+.TP
+\fB\-\-paired\fR
+The two filenames provided are paired\-end reads
+.TP
+\fB\-\-check\-names\fR
+Ensure each pair of reads have names that agree
+with each other; ignored if \fB\-\-paired\fR is not specified
+.TP
+\fB\-\-help\fR
+Print this message
+.TP
+\fB\-\-version\fR
+Print version information
+.PP
+If none of the *\-input or *\-compressed flags are specified, and the
+file is a regular file, automatic format detection is attempted.
diff --git a/debian/patches/kraken_tmp_dir.patch b/debian/patches/kraken_tmp_dir.patch
new file mode 100644
index 0000000..a69c1e7
--- /dev/null
+++ b/debian/patches/kraken_tmp_dir.patch
@@ -0,0 +1,44 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 09 Sep 2015 11:14:16 +0200
+Description: Some changes needed to differentiate packaging target dir and
+ install dir
+
+--- a/install_kraken.sh
++++ b/install_kraken.sh
+@@ -21,7 +21,7 @@ set -e
+
+ VERSION="0.10.5-beta"
+
+-if [ -z "$1" ] || [ -n "$2" ]
++if [ -z "$1" ] # || [ -n "$2" ]
+ then
+ echo "Usage: $(basename $0) KRAKEN_DIR"
+ exit 64
+@@ -38,20 +38,23 @@ fi
+ # on OS X.
+ export KRAKEN_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1")
+
+-mkdir -p "$KRAKEN_DIR"
+-make -C src install
++KRAKEN_TMP_DIR=`pwd`/debian/$2/$KRAKEN_DIR
++mkdir -p "$KRAKEN_TMP_DIR"
++# do this in debian/rules
++# make -C src install
+ for file in scripts/*
+ do
+ perl -pl -e 'BEGIN { while (@ARGV) { $_ = shift; ($k,$v) = split /=/, $_, 2; $H{$k} = $v } }'\
+ -e 's/#####=(\w+)=#####/$H{$1}/g' \
+ "KRAKEN_DIR=$KRAKEN_DIR" "VERSION=$VERSION" \
+- < "$file" > "$KRAKEN_DIR/$(basename $file)"
++ < "$file" > "$KRAKEN_TMP_DIR/$(basename $file)"
+ if [ -x "$file" ]
+ then
+- chmod +x "$KRAKEN_DIR/$(basename $file)"
++ chmod +x "$KRAKEN_TMP_DIR/$(basename $file)"
+ fi
+ done
+
++exit 0
+ echo
+ echo "Kraken installation complete."
+ echo
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..1cb33b0
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+kraken_tmp_dir.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..d230454
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,31 @@
+#!/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 $@ --sourcedirectory=src
+
+override_dh_link:
+ dh_link
+ for file in $(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/kraken* ; do \
+ if ! echo $${file} | grep -q '\.pm$$' ; then \
+ ln -s ../lib/$(DEBPKGNAME)/`basename $${file}` $(CURDIR)/debian/$(DEBPKGNAME)/usr/bin/`basename $${file}` ; \
+ fi \
+ done
+
+override_dh_auto_install:
+ dh_auto_install -- KRAKEN_DIR=$(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)
+ ./install_kraken.sh /usr/lib/$(DEBPKGNAME) $(DEBPKGNAME)
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..1c070c8
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Derrick E Wood and Steven L Salzberg
+ Title: "Kraken: ultrafast metagenomic sequence classification using exact alignments"
+ Journal: Genome Biol.
+ Year: 2014
+ Volume: 15
+ Number: 3
+ Pages: R46
+ DOI: 10.1186/gb-2014-15-3-r46
+ PMID: 24580807
+ URL: http://www.genomebiology.com/2014/15/3/R46
+ eprint: http://www.genomebiology.com/content/pdf/gb-2014-15-3-r46.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..db38634
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,7 @@
+version=3
+
+opts="uversionmangle=s{-beta}{~beta},filenamemangle=s{-beta}{~beta}"
+ https://github.com/DerrickWood/kraken/releases .*/archive/v(\d[\d.beta-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
+## FIXME: Mangling does not work. Here is an exampke from repmgr package. Try this later.
+## opts="uversionmangle=s/((?i)alpha|beta|rc)/~\L$1\E/,filenamemangle=s/(repmgr-.+?)((?i)alpha|beta|rc)/$1~\L$2\E/,pgpsigurlmangle=s/$/.asc/" \
\ No newline at end of file
--
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