[med-svn] [sumaclust] 01/06: Inject sumaclust
Andreas Tille
tille at debian.org
Wed Oct 18 17:47:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sumaclust.
commit b9d66096984567fa73948406ef4481e32798d55e
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 11 12:30:05 2015 +0000
Inject sumaclust
---
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 27 +++
debian/copyright | 519 +++++++++++++++++++++++++++++++++++++++++
debian/doc-base | 18 ++
debian/docs | 1 +
debian/install | 1 +
debian/manpages | 1 +
debian/patches/hardening.patch | 15 ++
debian/patches/series | 1 +
debian/rules | 23 ++
debian/source/format | 1 +
debian/sumaclust.1 | 88 +++++++
debian/watch | 9 +
14 files changed, 710 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..9a30ec8
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sumaclust (1.0.10-1) UNRELEASED; urgency=medium
+
+ * Initial upload to Debian (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Thu, 06 Aug 2015 15:30:54 +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..a9a78cb
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: sumaclust
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/sumaclust/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/sumaclust/trunk/
+Homepage: http://metabarcoding.org/sumaclust
+
+Package: sumaclust
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: fast and exact clustering of genomic sequences
+ With the development of next-generation sequencing, efficient tools are
+ needed to handle millions of sequences in reasonable amounts of time.
+ Sumaclust is a program developed by the LECA. Sumaclust aims to cluster
+ sequences in a way that is fast and exact at the same time. This tool
+ has been developed to be adapted to the type of data generated by DNA
+ metabarcoding, i.e. entirely sequenced, short markers. Sumaclust
+ clusters sequences using the same clustering algorithm as UCLUST and CD-
+ HIT. This algorithm is mainly useful to detect the 'erroneous' sequences
+ created during amplification and sequencing protocols, deriving from
+ 'true' sequences.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..19beeea
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,519 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Céline Mercier <celine.mercier at metabarcoding.org>
+Source: https://git.metabarcoding.org/obitools/sumaclust
+
+Files: *
+Copyright: 2013-2015 Tiayyba Riaz
+ Celine Mercier
+ Eric Coissac
+License: CeCILL-2
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: CeCILL-2
+
+License: CeCILL-2
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
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+ Article 12 - NEW VERSIONS OF THE AGREEMENT
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+ .
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+ Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
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+ that may arise during the performance of the Agreement.
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diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5252767
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,18 @@
+Document: sumaclust
+Title: Sumaclust: fast and exact clustering of sequences
+Author: Céline Mercier <celine.mercier at metabarcoding.org>
+Abstract: fast and exact clustering of genomic sequences
+ With the development of next-generation sequencing, efficient tools are
+ needed to handle millions of sequences in reasonable amounts of time.
+ Sumaclust is a program developed by the LECA. Sumaclust aims to cluster
+ sequences in a way that is fast and exact at the same time. This tool
+ has been developed to be adapted to the type of data generated by DNA
+ metabarcoding, i.e. entirely sequenced, short markers. Sumaclust
+ clusters sequences using the same clustering algorithm as UCLUST and CD-
+ HIT. This algorithm is mainly useful to detect the 'erroneous' sequences
+ created during amplification and sequencing protocols, deriving from
+ 'true' sequences.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/sumaclust/sumaclust_user_manual.pdf
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..a136337
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+*.pdf
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..0aebd39
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+sumaclust usr/bin
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/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..66953c0
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 05 Aug 2015 17:54:58 +0200
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -28,7 +28,7 @@ all: $(EXEC)
+ ifeq ($(CC),gcc)
+ LFLAGS = -fopenmp
+ else
+- LFLAGS =
++ LFLAGS = $(LDFLAGS)
+ endif
+
+ sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..814900f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..8d5022e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_clean:
+ dh_clean
+ #Upstream is very messy. Scrub out all the .svn stuff
+ #and .o files.
+ find sumalibs -name '*.[oa]' -delete
+
+override_dh_compress:
+ dh_compress --exclude=.pdf
+
+# May be it makes sense at some point in time to use *.md
+# source for the manpage - currently the result is not really
+# the usual manpage structure
+#override_dh_installman:
+# go-md2man -in=sumatra_user_manual.md -out=sumatra.1
\ No newline at end of file
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/sumaclust.1 b/debian/sumaclust.1
new file mode 100644
index 0000000..85120d8
--- /dev/null
+++ b/debian/sumaclust.1
@@ -0,0 +1,88 @@
+.TH SUMACLUST "1" "August 2015" "sumaclust 1.0.10" "User Commands"
+.SH NAME
+sumaclust \- star clustering of genetic sequences
+.SH SYNOPSIS
+.B sumaclust
+\fI[options] <dataset>\fR
+.SH DESCRIPTION
+.P
+With the development of next-generation sequencing, efficient tools are
+needed to handle millions of sequences in reasonable amounts of time.
+Sumaclust is a program developed by the LECA. Sumaclust aims to cluster
+sequences in a way that is fast and exact at the same time. This tool
+has been developed to be adapted to the type of data generated by DNA
+metabarcoding, i.e. entirely sequenced, short markers. Sumaclust
+clusters sequences using the same clustering algorithm as UCLUST and CD-
+HIT. This algorithm is mainly useful to detect the 'erroneous' sequences
+created during amplification and sequencing protocols, deriving from 'true'
+sequences.
+.SH OPTIONS
+.TP
+\fB\-h\fR
+[H]elp \- print <this> help
+.TP
+\fB\-l\fR
+: Reference sequence length is the shortest.
+.TP
+\fB\-L\fR
+Reference sequence length is the largest.
+.TP
+\fB\-a\fR
+Reference sequence length is the alignment length (default).
+.TP
+\fB\-n\fR
+Score is normalized by reference sequence length (default).
+.TP
+\fB\-r\fR
+: Raw score, not normalized.
+.TP
+\fB\-d\fR
+: Score is expressed in distance (default : score is expressed in similarity).
+.HP
+\fB\-t\fR ##.## : Score threshold for clustering. If the score is normalized and expressed in similarity (default),
+.IP
+it is an identity, e.g. 0.95 for an identity of 95%. If the score is normalized
+and expressed in distance, it is (1.0 \- identity), e.g. 0.05 for an identity of 95%.
+If the score is not normalized and expressed in similarity, it is the length of the
+Longest Common Subsequence. If the score is not normalized and expressed in distance,
+it is (reference length \- LCS length).
+Only sequences with a similarity above ##.## with the center sequence of a cluster
+are assigned to that cluster. Default: 0.97.
+.TP
+\fB\-e\fR
+Exact option: A sequence is assigned to the cluster with the center sequence presenting the
+highest similarity score > threshold, as opposed to the default 'fast' option where a sequence is
+assigned to the first cluster found with a center sequence presenting a score > threshold.
+.TP
+\fB\-R\fR ##
+Maximum ratio between the counts of two sequences so that the less abundant one can be considered
+as a variant of the more abundant one. Default: 1.0.
+.TP
+\fB\-p\fR ##
+Multithreading with ## threads using openMP.
+.TP
+\fB\-s\fR ####
+Sorting by ####. Must be 'None' for no sorting, or a key in the fasta header of each sequence,
+except for the count that can be computed (default : sorting by count).
+.TP
+\fB\-o\fR
+Sorting is in ascending order (default : descending).
+.TP
+\fB\-g\fR
+n's are replaced with a's (default: sequences with n's are discarded).
+.TP
+\fB\-B\fR ###
+Output of the OTU table in BIOM format is activated, and written to file ###.
+.TP
+\fB\-O\fR ###
+Output of the OTU map (observation map) is activated, and written to file ###.
+.TP
+\fB\-F\fR ###
+Output in FASTA format is written to file ### instead of standard output.
+.TP
+\fB\-f\fR
+Output in FASTA format is deactivated.
+.PP
+Argument : the nucleotide dataset to cluster
+.SH SEE ALSO
+http://metabarcoding.org/sumatra
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..af6f494
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,9 @@
+version=3
+
+https://git.metabarcoding.org/obitools/sumaclust/wikis/home .*/sumaclust/uploads/.*/sumaclust_v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
+# sumaclust is maintained in a Gitlab repository
+# https://wiki.debian.org/debian/watch#Gitlab
+# recommends something like this but it does not work
+# opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/<project>-$1\.tar\.gz/g \
+# https://git.metabarcoding.org/obitools/sumaclust/tags .*archive\.tar\.gz\?ref=v?(\d\S*)
--
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