[med-svn] [Git][med-team/tombo][master] 15 commits: python3-mappy now available
Andreas Tille
gitlab at salsa.debian.org
Wed Jun 24 13:31:39 BST 2020
Andreas Tille pushed to branch master at Debian Med / tombo
Commits:
a9aa99dd by Andreas Tille at 2020-06-24T10:16:38+02:00
python3-mappy now available
- - - - -
84951c86 by Andreas Tille at 2020-06-24T11:29:48+02:00
Add manpage
- - - - -
63a6543e by Andreas Tille at 2020-06-24T11:30:48+02:00
Install scripts
- - - - -
04329a29 by Andreas Tille at 2020-06-24T11:38:35+02:00
Add doc
- - - - -
3512b4d6 by Andreas Tille at 2020-06-24T11:41:43+02:00
Fix permissions
- - - - -
afd96d31 by Andreas Tille at 2020-06-24T11:44:00+02:00
Add recommends
- - - - -
ad9c8617 by Andreas Tille at 2020-06-24T13:22:58+02:00
Create sphinx documentation
- - - - -
c636df78 by Andreas Tille at 2020-06-24T13:35:52+02:00
Autopkgtest at least for the help system
- - - - -
82860e08 by Andreas Tille at 2020-06-24T13:43:29+02:00
Typo
- - - - -
ca75c3b4 by Andreas Tille at 2020-06-24T13:54:20+02:00
Separate doc package
- - - - -
4f46e416 by Andreas Tille at 2020-06-24T13:55:18+02:00
DEP3
- - - - -
fdd6753c by Andreas Tille at 2020-06-24T14:30:28+02:00
Syntax
- - - - -
985705ae by Andreas Tille at 2020-06-24T14:30:36+02:00
Fix installation
- - - - -
fbc2a851 by Andreas Tille at 2020-06-24T14:30:55+02:00
Fix section
- - - - -
e894e351 by Andreas Tille at 2020-06-24T14:31:26+02:00
Try hardening
- - - - -
12 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/createmanpages
- debian/patches/no_future.patch
- debian/rules
- debian/tests/run-unit-test
- + debian/tombo-doc.doc-base
- + debian/tombo-doc.install
- + debian/tombo.1
- + debian/tombo.install
- + debian/tombo.manpages
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,5 @@
tombo (1.5.1-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
- TODO: python3-mappy (from minimap2)
- blocked by https://salsa.debian.org/med-team/ksw2
+ * Initial release (Closes: #963596)
-- Andreas Tille <tille at debian.org> Mon, 15 Jun 2020 11:13:59 +0200
=====================================
debian/control
=====================================
@@ -8,8 +8,16 @@ Build-Depends: debhelper-compat (= 13),
python3-all-dev,
python3-setuptools,
cython3,
- python3-numpy,
- python3-tqdm
+ sphinx-doc,
+ python3-sphinx,
+ python3-sphinx-rtd-theme,
+ python3-sphinx-argparse,
+ python3-h5py <!nocheck>,
+ python3-mappy <!nocheck>,
+ python3-numpy <!nocheck>,
+ python3-scipy <!nocheck>,
+ python3-tqdm <!nocheck>,
+ python3-nose2 <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/tombo
Vcs-Git: https://salsa.debian.org/med-team/tombo.git
@@ -21,11 +29,25 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-h5py,
+ python3-mappy,
python3-numpy,
python3-scipy,
- python3-mappy,
python3-tqdm
+Recommends: python3-pyfaidx,
+ python3-rpy2
Description: identification of modified nucleotides from raw nanopore sequencing data
Tombo is a suite of tools primarily for the identification of modified
nucleotides from nanopore sequencing data. Tombo also provides tools for
the analysis and visualization of raw nanopore signal.
+
+Package: tombo-doc
+Architecture: all
+Section: doc
+Depends: ${sphinxdoc:Depends},
+ ${misc:Depends},
+Description: identification of modified nucleotides from raw nanopore sequencing data (doc)
+ Tombo is a suite of tools primarily for the identification of modified
+ nucleotides from nanopore sequencing data. Tombo also provides tools for
+ the analysis and visualization of raw nanopore signal.
+ .
+ This package contains the documentation for tombo.
=====================================
debian/copyright
=====================================
@@ -48,7 +48,6 @@ License: BSD-3-clause
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
Comment:
You are under no obligation whatsoever to provide any bug fixes,
patches, or upgrades to the features, functionality or performance of
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+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\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/${progname}.manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/patches/no_future.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 15 Jun 2020 11:13:59 +0200
+Description: Do not require future since we are using Python3 anyway
+
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,3 @@
=====================================
debian/rules
=====================================
@@ -1,26 +1,21 @@
#!/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
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export http_proxy='127.0.0.1:9'
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+
+overide_dh_fixperms:
+ dh_fixperms
+ find debian -name "*.model" -exec chmod -x \{\} \;
+
+override_dh_auto_build:
+ dh_auto_build
+ sphinx-build -N -bhtml docs docs/build
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# do_stuff_for_testing
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,19 +1,63 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=tombo
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # Double quote below to expand the temporary directory variable now versus
- # later is on purpose.
- # shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
cd "${AUTOPKGTEST_TMP}"
-#do_stuff_to_test_package#
+printf "********* Testing help commands **********\n"
+tombo -h || { echo 'Main tombo help failed. Likely a syntax error.' ; exit 1; }
+
+tombo resquiggle -h
+
+tombo preprocess annotate_raw_with_fastqs -h
+
+tombo filter clear_filters -h
+tombo filter stuck -h
+tombo filter level_coverage -h
+tombo filter q_score -h
+tombo filter raw_signal_matching -h
+tombo filter genome_locations -h
+
+tombo detect_modifications de_novo -h
+tombo detect_modifications alternative_model -h
+tombo detect_modifications model_sample_compare -h
+tombo detect_modifications level_sample_compare -h
+tombo detect_modifications aggregate_per_read_stats -h
+
+tombo text_output browser_files -h
+tombo text_output signif_sequence_context -h
+
+tombo plot max_coverage -h
+tombo plot genome_locations -h
+tombo plot motif_centered -h
+tombo plot max_difference -h
+tombo plot most_significant -h
+tombo plot motif_with_stats -h
+tombo plot per_read -h
+
+tombo plot roc -h
+tombo plot per_read_roc -h
+tombo plot kmer -h
+tombo plot cluster_most_significant -h
+
+tombo build_model estimate_scale -h
+tombo build_model event_resquiggle -h
+tombo build_model estimate_reference -h
+tombo build_model estimate_alt_reference -h
+
+cat <<EOT
+This test only tests the help system
+There is an extensive test in
+
+ tombo/tests/shell_tests.sh
+
+but this requires to download larger data
+sets which is not done for the moment.
+EOT
=====================================
debian/tombo-doc.doc-base
=====================================
@@ -0,0 +1,12 @@
+Document: tombo
+Title: documentation for tombo
+Author: Oxford Nanopore Technologies Ltd.
+Abstract: identification of modified nucleotides from raw nanopore sequencing data
+ Tombo is a suite of tools primarily for the identification of modified
+ nucleotides from nanopore sequencing data. Tombo also provides tools for
+ the analysis and visualization of raw nanopore signal.
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+Format: html
+Index: /usr/share/doc/tombo/html/index.html
+Files: /usr/share/doc/tombo/html/*
=====================================
debian/tombo-doc.install
=====================================
@@ -0,0 +1 @@
+docs/build/* usr/share/doc/tombo/html
=====================================
debian/tombo.1
=====================================
@@ -0,0 +1,45 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH TOMBO "1" "June 2020" "tombo 1.5.1" "User Commands"
+.SH NAME
+tombo \- identification of modified nucleotides from raw nanopore sequencing data
+.SH SYNOPSIS
+.B tombo
+[\-h] [\-v]
+{resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}
+\&...
+.SH DESCRIPTION
+Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
+.PP
+Tombo also provides tools for the analysis and visualization of raw nanopore signal.
+.SH "Tombo command groups (additional help available within each command group):"
+.TP
+resquiggle
+Re\-annotate raw signal with genomic alignment from existing basecalls.
+.TP
+preprocess
+Pre\-process nanopore reads for Tombo processing.
+.TP
+filter
+Apply filter to Tombo index file for specified criterion.
+.TP
+detect_modifications
+Perform statistical testing to detect non\-standard nucleotides.
+.TP
+text_output
+Output Tombo results in text files.
+.TP
+build_model
+Create canonical and alternative base Tombo models.
+.TP
+plot
+Save plots to visualize raw nanopore signal or testing results.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show Tombo version 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/tombo.install
=====================================
@@ -0,0 +1,2 @@
+usr
+scripts usr/share/tombo
=====================================
debian/tombo.manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a
--
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a
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