Updates to try to use a python3 compatible pyvcf

afonsoguerra · May 13, 2022 · 1873835 · 1873835
1 parent 671bd25
commit 1873835
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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
@@ -10,7 +10,7 @@
       install_requires=[
         'setuptools==58',
         'Jinja2',
-        'PyVCF',
+        'PyVCF3',
         'PyYAML'
       ],
       include_package_data=True,