[med-svn] r19834 - in trunk/packages: . sortmerna sortmerna/trunk sortmerna/trunk/debian sortmerna/trunk/debian/patches sortmerna/trunk/debian/scripts sortmerna/trunk/debian/source
Andreas Tille
tille at moszumanska.debian.org
Tue Aug 4 19:25:19 UTC 2015
Author: tille
Date: 2015-08-04 19:25:18 +0000 (Tue, 04 Aug 2015)
New Revision: 19834
Added:
trunk/packages/sortmerna/
trunk/packages/sortmerna/trunk/
trunk/packages/sortmerna/trunk/debian/
trunk/packages/sortmerna/trunk/debian/README_scripts.txt
trunk/packages/sortmerna/trunk/debian/changelog
trunk/packages/sortmerna/trunk/debian/compat
trunk/packages/sortmerna/trunk/debian/control
trunk/packages/sortmerna/trunk/debian/copyright
trunk/packages/sortmerna/trunk/debian/docs
trunk/packages/sortmerna/trunk/debian/install
trunk/packages/sortmerna/trunk/debian/patches/
trunk/packages/sortmerna/trunk/debian/patches/fix-interpreter-lines
trunk/packages/sortmerna/trunk/debian/patches/series
trunk/packages/sortmerna/trunk/debian/rules
trunk/packages/sortmerna/trunk/debian/scripts/
trunk/packages/sortmerna/trunk/debian/scripts/fetch_rrna_data.sh
trunk/packages/sortmerna/trunk/debian/source/
trunk/packages/sortmerna/trunk/debian/source/format
trunk/packages/sortmerna/trunk/debian/watch
Log:
Inject sortmerna as per BioLinux
Added: trunk/packages/sortmerna/trunk/debian/README_scripts.txt
===================================================================
--- trunk/packages/sortmerna/trunk/debian/README_scripts.txt (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/README_scripts.txt 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,9 @@
+The Debian package does not come with the large reference files needed to run
+the pipeline but they can be fetched easily by running the following:
+
+ $ sudo /usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh
+
+These files can also be recreated from the original sources. The following
+instructions are provided with the original source release of SortMeRNA:
+
+
Added: trunk/packages/sortmerna/trunk/debian/changelog
===================================================================
--- trunk/packages/sortmerna/trunk/debian/changelog (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/changelog 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,6 @@
+sortmerna (2.0-0biolinux1) trusty; urgency=medium
+
+ * Initial release.
+ * Lose memcheck.h from the build to simplify licensing.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 13 Feb 2015 18:00:35 +0000
Added: trunk/packages/sortmerna/trunk/debian/compat
===================================================================
--- trunk/packages/sortmerna/trunk/debian/compat (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/compat 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1 @@
+9
Added: trunk/packages/sortmerna/trunk/debian/control
===================================================================
--- trunk/packages/sortmerna/trunk/debian/control (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/control 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,34 @@
+Source: sortmerna
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9), dh-autoreconf
+Standards-Version: 3.9.6
+Homepage: http://bioinfo.lifl.fr/RNA/sortmerna/
+
+Package: sortmerna
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: python
+Description: tool for filtering, mapping and OTU-picking NGS reads
+ SortMeRNA is a biological sequence analysis tool for filtering, mapping and
+ OTU-picking NGS reads. The core algorithm is based on approximate seeds and
+ allows for fast and sensitive analyses of nucleotide sequences. The main
+ application of SortMeRNA is filtering rRNA from metatranscriptomic data.
+ Additional applications include OTU-picking and taxonomy assignation available
+ through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
+ SortMeRNA takes as input a file of reads (fasta or fastq format) and one or
+ multiple rRNA database file(s), and sorts apart rRNA and rejected reads into
+ two files specified by the user. Optionally, it can provide high quality local
+ alignments of rRNA reads against the rRNA database. SortMeRNA works with
+ Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and
+ BLAST-like alignments.
+ .
+ If you use SortMeRNA, please cite:
+ Kopylova E., Noé L. and Touzet H.,
+ "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in
+ metatranscriptomic data",
+ Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.
+
Added: trunk/packages/sortmerna/trunk/debian/copyright
===================================================================
--- trunk/packages/sortmerna/trunk/debian/copyright (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/copyright 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,69 @@
+Format: Something a bit like DEP5
+Files: src/ssw.c
+Copyright: Copyright (c) 2012-1015 Boston College.
+Author: Mengyao Zhao <zhangmp at bc.edu>
+License: The MIT License
+ Copyright (c) 2012-1015 Boston College.
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+
+Files: alp/*
+Author: John Spouge, Sergey Sheetlin
+License: Public Domain
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's offical duties as a United States Government employee and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
+
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+
+ Please cite the author in any work or product based on this material.
+
+Files: *
+Authors: jenya.kopylov at gmail.com, laurent.noe at lifl.fr, helene.touzet at lifl.fr
+Copyright: (C) 2012-2014 Bonsai Bioinformatics Research Group, LIFL and
+ INRIA Nord-Europe, France
+
+ OTU-picking extensions developed in the Knight Lab, BioFrontiers Institute,
+ University of Colorado at Boulder, Boulder, CO
+
+ SortMeRNA is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ SortMeRNA 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 Lesser General Public License for more details.
+
+ There is a copy of the LGPL3 in /usr/share/common-licenses
Added: trunk/packages/sortmerna/trunk/debian/docs
===================================================================
--- trunk/packages/sortmerna/trunk/debian/docs (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/docs 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1 @@
+*.pdf
Added: trunk/packages/sortmerna/trunk/debian/install
===================================================================
--- trunk/packages/sortmerna/trunk/debian/install (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/install 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,6 @@
+scripts /usr/share/sortmerna
+debian/scripts/* /usr/share/sortmerna/rRNA_databases/scripts
+rRNA_databases/scripts/* /usr/share/sortmerna/rRNA_databases/scripts
+tmp/README.txt /usr/share/sortmerna/rRNA_databases
+sortmerna /usr/bin
+indexdb_rna /usr/bin
Added: trunk/packages/sortmerna/trunk/debian/patches/fix-interpreter-lines
===================================================================
--- trunk/packages/sortmerna/trunk/debian/patches/fix-interpreter-lines (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/patches/fix-interpreter-lines 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,16 @@
+--- a/rRNA_databases/scripts/edit_U_to_T_rna.py
++++ b/rRNA_databases/scripts/edit_U_to_T_rna.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ # requires scikit bio [http://scikit-bio.org]
+
+ from skbio.parse.sequences import parse_fasta
+--- a/rRNA_databases/scripts/generate_databases.sh
++++ b/rRNA_databases/scripts/generate_databases.sh
+@@ -9,4 +9,4 @@
+ do
+ echo "sumaclust -l -p 40 -t ${id[i]} -F $rootdir/step4-c/${reference_db[i]} $rootdir/${reference_db[i]}"
+ echo "sumaclust -l -p 40 -t ${id[i]} -F $rootdir/step4-c/${reference_db[i]} $rootdir/${reference_db[i]}" | qsub -l nodes=1:ppn=40 -q mem4gbq -k oe -N ${db}_sumaclust; sleep 2
+-done
+\ No newline at end of file
++done
Added: trunk/packages/sortmerna/trunk/debian/patches/series
===================================================================
Added: trunk/packages/sortmerna/trunk/debian/rules
===================================================================
--- trunk/packages/sortmerna/trunk/debian/rules (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/rules 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,37 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with autoreconf
+
+override_dh_auto_configure:
+ dh_auto_configure -- --includedir=/usr/include/sortmerna
+
+override_dh_clean:
+ dh_clean
+ rm -f index/.tobuild
+ rm -f include/memcheck.h
+ rm -rf tmp
+
+override_dh_auto_build:
+ touch index/.tobuild
+ dh_auto_build
+ mkdir -p tmp
+ cat debian/README_scripts.txt rRNA_databases/README.txt > tmp/README.txt
+
+override_dh_auto_install:
+ #Skip this - do it manually
+ true
+
+override_dh_fixperms:
+ dh_fixperms
+ find debian/sortmerna -name '*.sh' -exec chmod +x '{}' ';'
+ find debian/sortmerna -name '*.py' -exec chmod -x '{}' ';'
Property changes on: trunk/packages/sortmerna/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/sortmerna/trunk/debian/scripts/fetch_rrna_data.sh
===================================================================
--- trunk/packages/sortmerna/trunk/debian/scripts/fetch_rrna_data.sh (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/scripts/fetch_rrna_data.sh 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,50 @@
+#!/bin/bash
+set -e
+set -u
+
+# I can't ship all the reference data in the DEB package. This script
+# will help you install it.
+
+# Hopefully soon I'll be able to deal with this by integrating with BioMaj3
+
+enterkey() {
+ if tty -s ; then
+ read -p "Press ENTER to continue, Ctrl+C to exit..." -r ignored
+ echo
+ fi
+}
+
+datadir=rRNA_databases
+
+if echo "$*" | grep -wq -- --here ; then
+ echo "Downloading to ./$datadir as --here was specified."
+ # No prompt needed here.
+ mkdir -p $datadir
+ cd $datadir
+elif [ "`id -u`" = 0 ] ; then
+ datadir=/usr/share/sortmerna/rRNA_databases
+ echo "Data will be downloaded to $datadir"
+ cd $datadir
+ umask 022
+ enterkey
+else
+ datadir="$HOME/sortmerna/rRNA_databases"
+ echo "Data will be downloaded to $datadir"
+ enterkey
+ mkdir -p "$datadir"
+ cd "$datadir"
+fi
+
+#Let us fetch! Thankfully no funny processing like we had to do with RDP-Classifier
+
+#tag=master
+tag=2.0
+
+for db in rfam-{5s,5.8s}-database-id98 \
+ silva-arc-{16s-id95,23s-id98} \
+ silva-bac-{16s-id90,23s-id98} \
+ silva-euk-{18s-id95,28s-id98} ; do
+ wget -c "https://github.com/biocore/sortmerna/raw/$tag/rRNA_databases/${db}.fasta"
+done
+
+echo DONE
Added: trunk/packages/sortmerna/trunk/debian/source/format
===================================================================
--- trunk/packages/sortmerna/trunk/debian/source/format (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/source/format 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/sortmerna/trunk/debian/watch
===================================================================
--- trunk/packages/sortmerna/trunk/debian/watch (rev 0)
+++ trunk/packages/sortmerna/trunk/debian/watch 2015-08-04 19:25:18 UTC (rev 19834)
@@ -0,0 +1,3 @@
+version=2
+# The file naming is inconsistent, so you'll need to look here manually:
+# http://bioinfo.lifl.fr/RNA/sortmerna/
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