# HG changeset patch
# User sanbi-uwc
# Date 1552396595 14400
# Node ID bbf9ab2ebee75dd6416de9a34f1064f6c105f41f
# Parent  5ec97cccb3feac9959d0e62578b59fb19da94253
planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c

diff -r 5ec97cccb3fe -r bbf9ab2ebee7 conda/0.1.5.tar.gz
Binary file conda/0.1.5.tar.gz has changed
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 conda/meta.yaml
--- 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
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil.egg-info/PKG-INFO
--- 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
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil.egg-info/SOURCES.txt
--- 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
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil.xml
--- 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>
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil/.confil.py.swp
Binary file confil/.confil.py.swp has changed
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil/__init__.pyc
Binary file confil/__init__.pyc has changed
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil/confil.pyc
Binary file confil/confil.pyc has changed
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil/kraken.py
--- 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))
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil/kraken.pyc
Binary file confil/kraken.pyc has changed
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 confil/report.pyc
Binary file confil/report.pyc has changed
diff -r 5ec97cccb3fe -r bbf9ab2ebee7 setup.py
--- a/setup.py	Mon Mar 11 07:18:34 2019 -0400
+++ b/setup.py	Tue Mar 12 09:16:35 2019 -0400
@@ -5,7 +5,7 @@
 
 setup(
     name='confil',
-    version='0.1.4',
+    version='0.1.5',
     url='https://github.com/COMBAT-TB/confil',
     description='Contamination filter',
     long_description=long_description,