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debian/README.test 0 → 100644
View file @ fb42c0ac
Notes on how this package can be tested.
────────────────────────────────────────
This package can be tested by running the provided test:
sh run-unit-test
in order to confirm its integrity.
debian/changelog
View file @ fb42c0ac
nanopolish (0.11.2-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* Run 2to3 to try Python3 port
nanopolish (0.11.2-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* New upstream release
Closes: #931784, #937105
* debhelper-compat 12
* Standards-Version: 4.4.0
* New upstream release, now we don't need the 2to3 patch
* Added patch to fixed #! for the python scripts
* Set upstream metadata fields: Repository.
-- Andreas Tille <tille@debian.org> Wed, 07 Aug 2019 20:38:25 +0200
[ Andreas Tille ]
* Standards-Version: 4.4.1
* Set upstream metadata fields: Bug-Database, Repository-Browse.
* Unify autopkgtest
-- Andreas Tille <tille@debian.org> Wed, 11 Dec 2019 15:48:48 +0100
nanopolish (0.11.1-1) unstable; urgency=medium
......
debian/control
View file @ fb42c0ac
......@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
libfast5-dev (>= 0.6.5),
libhts-dev,
libeigen3-dev
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/nanopolish
Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git
Homepage: https://github.com/jts/nanopolish
......
debian/docs
View file @ fb42c0ac
README.md
debian/tests/run-unit-test
debian/README.test
debian/patches/fix_remaining_python_interpreters.patch 0 → 100644
View file @ fb42c0ac
Author: Andreas Tille <tille@debian.org>
Bug-Debian: https://bugs.debian.org/931784
https://bugs.debian.org/937105
Bug-Upstream: https://github.com/jts/nanopolish/issues/626
Last-Update: Wed, 11 Dec 2019 15:02:32 +0100
Description: Fix some remaining interpreter names from python to python3
--- a/scripts/dropmodel.py
+++ b/scripts/dropmodel.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#! /usr/bin/python3
# Generate a new model with a lower k-mer size than the input model
import sys
--- a/scripts/import_ont_models_from_dir.sh
+++ b/scripts/import_ont_models_from_dir.sh
@@ -4,12 +4,12 @@ DIR=$1
for i in `ls $DIR`; do
echo "Processing", $DIR/$i
- python scripts/import_ont_model.py -i $DIR/$i -o etc/r9-models/ > new_files.txt
+ python3 scripts/import_ont_model.py -i $DIR/$i -o etc/r9-models/ > new_files.txt
done
for i in `cat new_files.txt`; do
echo "Dropping", $i
- python scripts/dropmodel.py -i $i
+ python3 scripts/dropmodel.py -i $i
done
rm new_files.txt
--- a/scripts/polya_training/hmmplot.py
+++ b/scripts/polya_training/hmmplot.py
@@ -3,7 +3,7 @@
Plot a random segmentation from a dataset.
Usage:
- $ python polya.out.tsv reads.fastq.readdb.index
+ $ python3 polya.out.tsv reads.fastq.readdb.index
"""
import h5py
import pandas as pd
--- a/scripts/polya_training/workflow.md
+++ b/scripts/polya_training/workflow.md
@@ -57,7 +57,7 @@ The following files are included:
* `retrain_emission.py`: take the arrays from a run of `dump_signal.py` and output the coefficients and parameters
of a gaussian mixture model for each segment.
-Run `python <SCRIPT> --help` for further usage instructions for each script.
+Run `python3 <SCRIPT> --help` for further usage instructions for each script.
The files above required a suite of numerical packages to be installed as dependencies. A full list of dependencies,
-in a conda-compatible environment file, is available at `hmmplot/environment.yml`.
\ No newline at end of file
+in a conda-compatible environment file, is available at `hmmplot/environment.yml`.
--- a/scripts/reestimate_polya_emissions.py
+++ b/scripts/reestimate_polya_emissions.py
@@ -5,7 +5,7 @@ underlying kmer models (with the newer T
infer the best new parameters for the HMM emissions.
Usage:
-$ python reestimate_polya_emissions.py samples.old.tsv seg.old.tsv samples.new.tsv
+$ python3 reestimate_polya_emissions.py samples.old.tsv seg.old.tsv samples.new.tsv
where:
* `samples.old.tsv` is the output of `nanopolish polya -vv [...] | grep 'polya-samples'`,
generated by the **old** kmer models;
debian/patches/series
View file @ fb42c0ac
add-shebang-to-script.patch
reproducible.patch
add_interp
fix_remaining_python_interpreters.patch
debian/rules
View file @ fb42c0ac
......@@ -35,7 +35,7 @@ override_dh_install:
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $${pl} ; \
done
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \
sed -i '1s?^#!.*python?#!/usr/bin/python?' $${pl} ; \
sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' $${pl} ; \
done
override_dh_fixperms:
......
debian/scripts/nanopolish_makerange
View file @ fb42c0ac
#!/bin/sh
/usr/bin/python /usr/lib/nanopolish/nanopolish_makerange.py $@
/usr/bin/python3 /usr/lib/nanopolish/nanopolish_makerange.py $@
debian/tests/control
View file @ fb42c0ac
Tests: main
Tests: run-unit-test
Depends: @
debian/tests/main deleted 100755 → 0
View file @ b32c1f45
#!/bin/sh
set -e
cd $ADTTMP
# The ./test/data path is hard-coded into the nanopolish_test program
mkdir test
cp -r /usr/share/doc/nanopolish/examples/data $ADTTMP/test/
find $ADTTMP/test/data -name '*.gz' | xargs -r gunzip
/usr/lib/nanopolish/nanopolish_test
debian/tests/run-unit-test 0 → 100644
View file @ fb42c0ac
#!/bin/bash
set -e
pkg=nanopolish
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cd ${AUTOPKGTEST_TMP}
# The ./test/data path is hard-coded into the nanopolish_test program
mkdir test
cp -r /usr/share/doc/${pkg}/examples/data ${AUTOPKGTEST_TMP}/test
find ${AUTOPKGTEST_TMP}/test -name '*.gz' | xargs -r gunzip
/usr/lib/nanopolish/nanopolish_test
debian/upstream/metadata
View file @ fb42c0ac
......@@ -8,3 +8,5 @@ Registry:
- Name: conda:bioconda
Entry: nanopolish
Repository: https://github.com/jts/nanopolish.git
Bug-Database: https://github.com/jts/nanopolish/issues
Repository-Browse: https://github.com/jts/nanopolish