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Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 05 Oct 2022 10:30:56 +0200
Description: Fix path to R script
--- a/python/run_FastQTL_threaded.py
+++ b/python/run_FastQTL_threaded.py
@@ -91,7 +91,7 @@ with cd(args.output_dir):
# calculate q-values (R script also adds header)
print('Calculating q-values', flush=True)
- cmd = 'Rscript '+os.path.join(fastqtl_dir, 'R', 'calculateSignificanceFastQTL.R')\
+ cmd = 'Rscript '+os.path.join('/usr/share/fastqtl', 'calculateSignificanceFastQTL.R')\
+' '+args.prefix+'.txt.gz '+str(args.fdr)+' '+args.prefix+'.egenes.txt.gz'
if args.qvalue_lambda is not None:
cmd += ' --lambda '+args.qvalue_lambda
--- a/python/merge_chunks.py
+++ b/python/merge_chunks.py
@@ -41,7 +41,7 @@ with cd(args.output_dir):
# calculate q-values (R script also adds header)
print('Calculating q-values', flush=True)
- cmd = 'Rscript '+os.path.join(fastqtl_dir, 'R', 'calculateSignificanceFastQTL.R')\
+ cmd = 'Rscript '+os.path.join('/usr/share/fastqtl', 'calculateSignificanceFastQTL.R')\
+' '+args.prefix+'.txt.gz '+str(args.fdr)+' '+args.prefix+'.egenes.txt.gz'
if args.lambda_qvalue is not None:
cmd += ' --lambda '+args.lambda_qvalue
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