[med-svn] [seqtools] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Thu Oct 19 15:34:09 UTC 2017
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tille pushed a commit to branch master
in repository seqtools.
commit e246ec83b9a333432f8a71bfb1d7472bfa18223d
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 19 17:33:25 2017 +0200
Initial packaging
---
debian/belvu.install | 1 +
debian/blixem.install | 1 +
debian/changelog | 8 +++
debian/compat | 1 +
debian/control | 118 +++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 16 ++++++
debian/dotter.install | 1 +
debian/libseqtools.install | 2 +
debian/rules | 22 +++++++++
debian/source/format | 1 +
debian/upstream/metadata | 42 ++++++++++++++++
debian/watch | 4 ++
12 files changed, 217 insertions(+)
diff --git a/debian/belvu.install b/debian/belvu.install
new file mode 100644
index 0000000..e55b614
--- /dev/null
+++ b/debian/belvu.install
@@ -0,0 +1 @@
+usr/bin/belvu
diff --git a/debian/blixem.install b/debian/blixem.install
new file mode 100644
index 0000000..95e076c
--- /dev/null
+++ b/debian/blixem.install
@@ -0,0 +1 @@
+usr/bin/blixem*
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..edd8fe1
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,8 @@
+seqtools (4.44.1-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+ TODO / clarify: relation to
+ acedb-other-belvu, acedb-other-dotter (both seem outdated but occupy
+ the same name while providing somehow same functionality
+
+ -- Andreas Tille <tille at debian.org> Thu, 19 Oct 2017 16:27:56 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..197e25e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,118 @@
+Source: seqtools
+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 (>= 10),
+ libgtk2.0-dev,
+ libsqlite3-dev,
+ libcurl4-openssl-dev | libcurl4-dev
+Standards-Version: 4.1.1
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/seqtools.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/seqtools.git
+Homepage: http://www.sanger.ac.uk/science/tools/seqtools
+
+Package: libseqtools
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: library for visualising sequence alignments
+ The SeqTools package contains three tools for visualising sequence
+ alignments: Blixem, Dotter and Belvu.
+ .
+ This package contains the library all three tools are linked against.
+
+Package: belvu
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: multiple sequence alignment viewer and phylogenetic tool
+ Belvu is a multiple sequence alignment viewer and phylogenetic tool with
+ an extensive set of user-configurable modes to color residues.
+ .
+ * View multiple sequence alignments.
+ * Residues can be coloured by conservation, with user-configurable
+ cutoffs and colours.
+ * Residues can be coloured by residue type (user-configurable).
+ * Colour schemes can be imported or exported.
+ * Swissprot (or PIR) entries can be fetched by double clicking.
+ * The position in the alignment can be easily tracked.
+ * Manual deletion of rows and columns.
+ * Automatic editing of rows and columns based on customisable criteria:
+ - removal of all-gap columns;
+ - removal of all gaps;
+ - removal of redundant sequences;
+ - removal of a column by a user-specified percentage of gaps;
+ - filtering of sequences by percent identity;
+ - removal of sequences by a user-specified percentage of gaps;
+ - removal of partial sequences (those starting or ending with
+ gaps); and
+ - removal of columns by conservation (with user-specified
+ upper/lower cutoffs).
+ * The alignment can be saved in Stockholm, Selex, MSF or FASTA format.
+ * Distance matrices between sequences can be generated using a variety
+ of distance metrics.
+ * Distance matrices can be imported or exported.
+ * Phylogenetic trees can be constructed based on various distance-based
+ tree reconstruction algorithms.
+ * Trees can be saved in New Hampshire format.
+ * Belvu can perform bootstrap phylogenetic reconstruction.
+
+Package: blixem
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: interactive browser of sequence alignments
+ Blixem is an interactive browser of sequence alignments that have been
+ stacked up in a "master-slave" multiple alignment; it is not a 'true'
+ multiple alignment but a 'one-to-many' alignment.
+ .
+ * Overview section showing the positions of genes and alignments around
+ the alignment window
+ * Detail section showing the actual alignment of protein or nucleotide
+ sequences to the genomic DNA sequence.
+ * View alignments against both strands of the reference sequence.
+ * View sequences in nucleotide or protein mode; in protein mode, Blixem
+ will display the three-frame translation of the reference sequence.
+ * Residues are highlighted in different colours depending on whether
+ they are an exact match, conserved substitution or mismatch.
+ * Gapped alignments are supported, with insertions and deletions being
+ highlighted in the match sequence.
+ * Matches can be sorted and filtered.
+ * SNPs and other variations can be highlighted in the reference
+ sequence.
+ * Poly(A) tails can be displayed and poly(A) signals highlighted in the
+ reference sequence.
+
+Package: dotter
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: detailed comparison of two genomic sequences
+ Dotter is a graphical dot-matrix program for detailed comparison of two
+ sequences.
+ .
+ * Every residue in one sequence is compared to every residue in the
+ other, and a matrix of scores is calculated.
+ * One sequence is plotted on the x-axis and the other on the y-axis.
+ * Noise is filtered out so that alignments appear as diagonal lines.
+ * Pairwise scores are averaged over a sliding window to make the score
+ matrix more intelligible.
+ * The averaged score matrix forms a three-dimensional landscape,
+ with the two sequences in two dimensions and the height of the
+ peaks in the third. This landscape is projected onto two
+ dimensions using a grey-scale image - the darker grey of a peak,
+ the higher the score is.
+ * The contrast and threshold of the grey-scale image can be adjusted
+ interactively, without having to recalculate the score matrix.
+ * An Alignment Tool is provided to examine the sequence alignment that
+ the grey-scale image represents.
+ * Known high-scoring pairs can be loaded from a GFF file and overlaid
+ onto the plot.
+ * Gene models can be loaded from GFF and displayed alongside the
+ relevant axis.
+ * Compare a sequence against itself to find internal repeats.
+ * Find overlaps between multiple sequences by making a dot-plot of all
+ sequences versus themselves.
+ * Run Dotter in batch mode to create large, time-consuming dot-plots as
+ a background process.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0ca1092
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,16 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+Comment: **** Before manually editing this file you should give ****
+ scan-copyrights
+ **** available in cme + lib-config-model-dpkg-perl ****
+ **** package a try. For existing copyright files try ****
+ cme update dpkg-copyright
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2017 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/dotter.install b/debian/dotter.install
new file mode 100644
index 0000000..41f36b5
--- /dev/null
+++ b/debian/dotter.install
@@ -0,0 +1 @@
+usr/bin/dotter
diff --git a/debian/libseqtools.install b/debian/libseqtools.install
new file mode 100644
index 0000000..4418816
--- /dev/null
+++ b/debian/libseqtools.install
@@ -0,0 +1,2 @@
+usr/lib
+usr/include
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..62983db
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+# this provides:
+# DEB_SOURCE: the source package name
+# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
+# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
+# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
+# DEB_VERSION_UPSTREAM: the package's upstream version
+# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
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..0b6419d
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,42 @@
+Reference:
+ - Author: Gemma Barson and Ed Griffiths
+ Title: "SeqTools: visual tools for manual analysis of sequence alignments"
+ Journal: BMC Research Notes
+ Year: 2016
+ Volume: 9
+ Pages: 39
+ DOI: 10.1186/s13104-016-1847-3
+ PMID: 26801397
+ URL: https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1847-3
+ eprint: https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-016-1847-3?site=bmcresnotes.biomedcentral.com
+ - Author: Erik LL Sonnhammer and Volker Hollich
+ Title: "Scoredist: A simple and robust protein sequence distance estimator"
+ Journal: BMC Bioinformatics
+ Year: 2005
+ Volume: 6
+ Pages: 108
+ DOI: 10.1186/1471-2105-6-108
+ PMID: 15857510
+ URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-108
+ eprint: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-6-108?site=bmcbioinformatics.biomedcentral.com
+ - Author: Erik LL Sonnhammer and Richard Durbin
+ Title: "A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis"
+ Journal: Gene
+ Year: 1995
+ Volume: 167
+ Number: 1-2
+ Pages: GC1-10
+ DOI: 10.1016/0378-1119(95)00714-8
+ PMID: 8566757
+ URL: http://www.sciencedirect.com/science/article/pii/0378111995007148
+ Debian-Package: dotter
+ - Author: Erik LL Sonnhammer and Richard Durbin
+ Title: "A workbench for large-scale sequence homology analysis"
+ Journal: Comput Appl Biosci.
+ Year: 1994
+ Volume: 10
+ Number: 3
+ Pages: 301-7
+ DOI: 10.1093/bioinformatics/10.3.301
+ PMID: 7922687
+ URL: https://www.researchgate.net/publication/220263362_A_Workbench_for_large-scale_sequence_homology_analysis
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..9788522
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts=passive \
+ ftp://ftp.sanger.ac.uk/pub/resources/software/seqtools/PRODUCTION/seqtools-@ANY_VERSION@@ARCHIVE_EXT@
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