Author: Steffen Moeller
Last-Update: 2020-11-13 23:16:13 +0100
Description: Fix interpreter name to python3

Index: bcbio/scripts/bcbio_fastq_umi_prep.py
===================================================================
--- bcbio.orig/scripts/bcbio_fastq_umi_prep.py
+++ bcbio/scripts/bcbio_fastq_umi_prep.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 """Convert fastq inputs into paired inputs with UMIs in read names.
 
 Handles three cases:
Index: bcbio/scripts/bcbio_nextgen_install.py
===================================================================
--- bcbio.orig/scripts/bcbio_nextgen_install.py
+++ bcbio/scripts/bcbio_nextgen_install.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 """Automatically install required tools and data to run bcbio-nextgen pipelines.
 
 This automates the steps required for installation and setup to make it easier to get started with
Index: bcbio/scripts/bcbio_nextgen.py
===================================================================
--- bcbio.orig/scripts/bcbio_nextgen.py
+++ bcbio/scripts/bcbio_nextgen.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python -Es
+#!/usr/bin/python3 -s
 """Run an automated analysis pipeline for high throughput sequencing data.
 
 Handles runs in local or distributed mode based on the command line or
Index: bcbio/scripts/bcbio_setup_genome.py
===================================================================
--- bcbio.orig/scripts/bcbio_setup_genome.py
+++ bcbio/scripts/bcbio_setup_genome.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python -Es
+#!/usr/bin/python3 -Es
 """
 Script to set up a custom genome for bcbio-nextgen
 """
Index: bcbio/scripts/cwl/arvados_bcbio_runtimes.py
===================================================================
--- bcbio.orig/scripts/cwl/arvados_bcbio_runtimes.py
+++ bcbio/scripts/cwl/arvados_bcbio_runtimes.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 """Summarize runtimes for bcbio Arvados CWL runs.
 
 Usage:
Index: bcbio/scripts/cwltool2wdl.py
===================================================================
--- bcbio.orig/scripts/cwltool2wdl.py
+++ bcbio/scripts/cwltool2wdl.py
@@ -1,4 +1,4 @@
-#!/bin/env python
+#!/usr/bin/python3
 """Exploratory code to convert bcbio generated CWL into WDL.
 
 Uses cwltool parser to parse input CWL then, calls out to cwl2wdl
Index: bcbio/tests/run_tests.sh
===================================================================
--- bcbio.orig/tests/run_tests.sh
+++ bcbio/tests/run_tests.sh
@@ -24,7 +24,8 @@ else
 fi
 
 unset PYTHONHOME
-unset PYTHONPATH
+export PATH=$(pwd)/scripts:/usr/lib/debian-med/bin:$PATH
+export PYTHONPATH=$(pwd)
 export PYTHONNOUSERSITE=1
 # Ensure version.py exists in raw cloned bcbio directory
 if [ -d "../bcbio/pipeline" ]; then