From 18738359aaa49daa60d52c6c86844dc118abe540 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Afonso=20Guerra-Assun=C3=A7=C3=A3o?= Date: Fri, 13 May 2022 08:20:34 +0100 Subject: [PATCH] Updates to try to use a python3 compatible pyvcf --- Singularity | 2 +- scripts/snpEffBuildAndRun | 4 ++-- setup.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Singularity b/Singularity index 9a846b8..d7655e8 100644 --- a/Singularity +++ b/Singularity @@ -15,7 +15,7 @@ From: python:3 rm -rf /sanger-pathogens/SnpEffWrapper/build/clinEff/ rm -rf /sanger-pathogens/SnpEffWrapper/build/*.zip python3 -m pip install setuptools==58 - python3 -m pip install pyvcf + python3 -m pip install pyvcf3 python3 -m pip install /sanger-pathogens/SnpEffWrapper %runscript diff --git a/scripts/snpEffBuildAndRun b/scripts/snpEffBuildAndRun index a243a26..cb984fa 100755 --- a/scripts/snpEffBuildAndRun +++ b/scripts/snpEffBuildAndRun @@ -7,8 +7,8 @@ import sys #Early morning hacks... #sys.path.append('/sanger-pathogens/SnpEffWrapper/') -sys.path.append('/usr/local/lib/python3.10/site-packages/') -sys.path.append('/usr/local/lib/python3.10/site-packages/vcf/') +#sys.path.append('/usr/local/lib/python3.10/site-packages/') +#sys.path.append('/usr/local/lib/python3.10/site-packages/vcf/') from snpEffWrapper.wrapper import annotate_vcf, check_and_amend_executables diff --git a/setup.py b/setup.py index b13ecaa..d6ba651 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ install_requires=[ 'setuptools==58', 'Jinja2', - 'PyVCF', + 'PyVCF3', 'PyYAML' ], include_package_data=True,