[med-svn] [Git][med-team/augur][master] 6 commits: Seems rethinkdb is not needed any more
Andreas Tille
gitlab at salsa.debian.org
Tue Mar 24 06:02:13 GMT 2020
Andreas Tille pushed to branch master at Debian Med / augur
Commits:
b619c815 by Andreas Tille at 2020-03-23T11:47:11+01:00
Seems rethinkdb is not needed any more
- - - - -
a4cc40eb by Andreas Tille at 2020-03-23T11:58:31+01:00
Add build time test
- - - - -
d76804ef by Andreas Tille at 2020-03-23T11:59:10+01:00
Remove useless license file
- - - - -
f319f907 by Andreas Tille at 2020-03-23T15:03:27+01:00
Update manpage
- - - - -
e552534c by Andreas Tille at 2020-03-23T15:04:40+01:00
Upload to new
- - - - -
4e706aef by Andreas Tille at 2020-03-24T07:01:53+01:00
Fix license
- - - - -
7 changed files:
- + debian/augur.1
- debian/changelog
- debian/control
- debian/copyright
- debian/createmanpages
- + debian/manpages
- debian/rules
Changes:
=====================================
debian/augur.1
=====================================
@@ -0,0 +1,90 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH AUGUR "1" "March 2020" "augur 6.4.2" "User Commands"
+.SH NAME
+augur \- pipeline components for real-time virus analysis
+.SH SYNOPSIS
+.B augur
+[\-h] {parse,filter,mask,align,tree,refine,ancestral,translate,reconstruct\-sequences,clades,traits,sequence\-traits,lbi,distance,titers,frequencies,export,validate,version,import}
+\&...
+.SH DESCRIPTION
+Augur: A bioinformatics toolkit for phylogenetic analysis.
+.SH OPTIONS
+.SS "positional arguments:"
+.IP
+{parse,filter,mask,align,tree,refine,ancestral,translate,reconstruct\-sequences,clades,traits,sequence\-traits,lbi,distance,titers,frequencies,export,validate,version,import}
+.TP
+parse
+Parse delimited fields from FASTA sequence names into
+a TSV and FASTA file.
+.TP
+filter
+Filter and subsample a sequence set.
+.TP
+mask
+Mask specified sites from a VCF file.
+.TP
+align
+Align multiple sequences from FASTA.
+.TP
+tree
+Build a tree using a variety of methods.
+.TP
+refine
+Refine an initial tree using sequence metadata.
+.TP
+ancestral
+Infer ancestral sequences based on a tree.
+.TP
+translate
+Translate gene regions from nucleotides to amino
+acids.
+.TP
+reconstruct\-sequences
+Reconstruct alignments from mutations inferred on the
+tree
+.TP
+clades
+Assign clades to nodes in a tree based on amino\-acid
+or nucleotide signatures.
+.TP
+traits
+Infer ancestral traits based on a tree.
+.TP
+sequence\-traits
+Annotate sequences based on amino\-acid or nucleotide
+signatures.
+.TP
+lbi
+Calculate LBI for a given tree and one or more sets of
+parameters.
+.TP
+distance
+Calculate the distance between sequences across entire
+genes or at a predefined subset of sites.
+.TP
+titers
+Annotate a tree with actual and inferred titer
+measurements.
+.TP
+frequencies
+infer frequencies of mutations or clades
+.TP
+export
+Export JSON files suitable for visualization with
+auspice.
+.TP
+validate
+Validate files related to augur consumption or export.
+.TP
+version
+Print the version of augur.
+.TP
+import
+Import analyses into augur pipeline from other systems
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-augur (6.4.2-1) UNRELEASED; urgency=medium
+augur (6.4.2-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #954777)
- -- Andreas Tille <tille at debian.org> Fri, 20 Mar 2020 15:27:37 +0100
+ -- Andreas Tille <tille at debian.org> Mon, 23 Mar 2020 15:03:35 +0100
=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 12),
dh-python,
python3-all,
python3-setuptools,
+ python3-pytest <!nocheck>,
python3-biopython <!nocheck>,
python3-jsonschema <!nocheck>,
python3-packaging <!nocheck>,
@@ -33,8 +34,8 @@ Depends: ${python3:Depends},
python3-seaborn (>= 0.6.0),
python3-treetime,
seqmagick,
- python3-ipdb
-# rethinkdb==1.13.0-2,
+ python3-ipdb,
+ python3-bcbio-gff
Description: pipeline components for real-time virus analysis
The nextstrain project is an attempt to make flexible informatic
pipelines and visualization tools to track ongoing pathogen evolution as
=====================================
debian/copyright
=====================================
@@ -4,13 +4,13 @@ Source: https://github.com/nextstrain/augur
Files: *
Copyright: 2014-2016 Trevor Bedford and Richard Neher
-License: AGPL-3+
+License: AGPL-3
Files: debian/*
Copyright: 2017 Andreas Tille <tille at debian.org>
-License: AGPL-3+
+License: AGPL-3
-License: AGPL-3+
+License: AGPL-3
GNU Affero General Public License v3.0
.
Permissions of this strongest copyleft license are conditioned on making
=====================================
debian/createmanpages
=====================================
@@ -1,34 +1,28 @@
#!/bin/sh
-MANDIR=debian/mans
+MANDIR=debian
mkdir -p $MANDIR
VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
-AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
-can be used for any other usage of the program.
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
"
-progname=ancestral_reconstruction
-help2man --no-info --no-discard-stderr \
- --name='Reconstructs ancestral sequences and maps mutations to the tree' \
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
-progname=temporal_signal
-help2man --no-info --no-discard-stderr \
- --name="Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of a tree" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
-
-progname=timetree_inference
-help2man --no-info --no-discard-stderr \
- --name='Reconstructs ancestral sequences and infers a molecular clock tree' \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+echo "$MANDIR/*.1" > debian/manpages
cat <<EOT
Please enhance the help2man output.
The following web page might be helpful in doing so:
http://liw.fi/manpages/
EOT
-
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/rules
=====================================
@@ -5,3 +5,7 @@ export LC_ALL=C.UTF-8
%:
dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_install:
+ dh_install
+ find debian -name LICENSE.txt -delete
View it on GitLab: https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9
--
View it on GitLab: https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9
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