Mercurial > repos > sanbi-uwc > confil
changeset 13:bbf9ab2ebee7 draft default tip
planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c
author | sanbi-uwc |
---|---|
date | Tue, 12 Mar 2019 09:16:35 -0400 |
parents | 5ec97cccb3fe |
children | |
files | conda/0.1.5.tar.gz conda/meta.yaml confil.egg-info/PKG-INFO confil.egg-info/SOURCES.txt confil.xml confil/.confil.py.swp confil/__init__.pyc confil/confil.pyc confil/kraken.py confil/kraken.pyc confil/report.pyc setup.py |
diffstat | 12 files changed, 11 insertions(+), 19 deletions(-) [+] |
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--- a/conda/meta.yaml Mon Mar 11 07:18:34 2019 -0400 +++ b/conda/meta.yaml Tue Mar 12 09:16:35 2019 -0400 @@ -1,5 +1,5 @@ -{% set version = "0.1.4" %} -{% set sha256 = "1ebbb14e64e057d6b58f4942a7b1dbf9e53f4ab741709b0ecfcb8d358fb8848e" %} +{% set version = "0.1.5" %} +{% set sha256 = "9e92cf4ebbbad9c0571cbcfc014e824cd74a135e5449085205269c3b6f40209b" %} package: name: confil
--- a/confil.egg-info/PKG-INFO Mon Mar 11 07:18:34 2019 -0400 +++ b/confil.egg-info/PKG-INFO Tue Mar 12 09:16:35 2019 -0400 @@ -1,12 +1,9 @@ -Metadata-Version: 1.0 +Metadata-Version: 2.1 Name: confil -Version: 0.1.2.dev20190304 +Version: 0.1.3.dev20190307 Summary: Contamination filter Home-page: https://github.com/COMBAT-TB/confil -Author: UNKNOWN -Author-email: UNKNOWN License: UNKNOWN -Description-Content-Type: text/markdown Description: # confil [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil) @@ -36,3 +33,4 @@ Keywords: contamination,filter Platform: UNKNOWN +Description-Content-Type: text/markdown
--- a/confil.egg-info/SOURCES.txt Mon Mar 11 07:18:34 2019 -0400 +++ b/confil.egg-info/SOURCES.txt Tue Mar 12 09:16:35 2019 -0400 @@ -3,13 +3,10 @@ setup.py confil/__init__.py confil/confil.py -confil/kraken.py -confil/report.py confil.egg-info/PKG-INFO confil.egg-info/SOURCES.txt confil.egg-info/dependency_links.txt confil.egg-info/entry_points.txt confil.egg-info/requires.txt confil.egg-info/top_level.txt -test/test_report.py test/test_runner.py \ No newline at end of file
--- a/confil.xml Mon Mar 11 07:18:34 2019 -0400 +++ b/confil.xml Tue Mar 12 09:16:35 2019 -0400 @@ -1,6 +1,6 @@ <tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy0"> <macros> - <token name="@VERSION@">0.1.4</token> + <token name="@VERSION@">0.1.5</token> </macros> <requirements> <requirement type="package" version="@VERSION@">confil</requirement>
--- a/confil/kraken.py Mon Mar 11 07:18:34 2019 -0400 +++ b/confil/kraken.py Tue Mar 12 09:16:35 2019 -0400 @@ -42,13 +42,10 @@ # click.secho("Executing mock_cmd: \n{}\n".format(split(cmd)), fg='red') p = Popen(split(cmd), stdout=PIPE, stderr=PIPE, close_fds=True) - while True: - output = p.stdout.readline() - if output == '' and p.poll() is not None: - break - if output: - click.echo(output) - returncode = p.poll() + (output, _) = p.communicate() + if output: + click.echo(output) + returncode = p.wait() if returncode != 0: error = p.stderr.readline() raise OSError("Kraken2 launch error:\n{}\n".format(error))