phaser bugs

jaredgk · Oct 20, 2019 · bf263be · bf263be
1 parent 8a01bf5
commit bf263be
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -27,7 +27,8 @@ before_install:
   - conda install -c anaconda rpy2
   - conda install -c bioconda tabix 
   - conda install -c bioconda bcftools
-  - conda install -c bioconda vcftools 
+  - conda install -c bioconda vcftools
+  - conda install -c bioconda shapeit 
   - conda install -c bioconda pysam
   - conda install -c anaconda scikit-learn
   - conda install -c anaconda cython 

diff --git a/pgpipe/vcf_phase.py b/pgpipe/vcf_phase.py
@@ -746,7 +746,7 @@ def run (passed_arguments = []):
             phase_call_args.append(chr_arg)
 
         # Call beagle wrapper
-        call_beagle(beagle_path, list(map(str, phase_call_args)), phase_args.out_prefix, phase_args.out_format)
+        call_beagle(phase_args.beagle_path, list(map(str, phase_call_args)), phase_args.out_prefix, phase_args.out_format)
 
         # Rename log using phased_output
         shutil.move(phase_args.out_prefix + '.log', phased_output + '.log')