Commit b16035ec authored by Gonzalo S Nido's avatar Gonzalo S Nido
Browse files

Minor cosmetic fixes

parent d1ae404e
......@@ -44,7 +44,7 @@ N_proc=`expr $( grep -c processor /proc/cpuinfo ) / 2`
# 1) Obtain GRCh38 human genome from ENCODE
echo "1/8 - Downloading GRCh38 reference..."
wget -o wget.log --show-progress -O ${grch38_fasta}.gz ${GRCH38_url}
wget --show-progress -O ${grch38_fasta}.gz ${GRCH38_url}
echo " Decompressing GRCh38 reference..."
gunzip -f ${grch38_fasta}.gz
......@@ -52,7 +52,7 @@ gunzip -f ${grch38_fasta}.gz
# 2) Obtain Lambda genome
echo "2/8 - Downloading Lambda genome..."
wget -a wget.log --show-progress -O ${lambda_fasta}.gz ${LAMBDA_url}
wget --show-progress -O ${lambda_fasta}.gz ${LAMBDA_url}
echo " Decompressing Lambda reference..."
gunzip -f ${lambda_fasta}.gz
......
......@@ -40,8 +40,8 @@ set -e
# Ensure reference files/indices are there, download and index otherwise
if [[ ! -s ${b38_ref}/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa ]]; then
echo "Reference files not found. Downloading and indexing..."
bash ${generate_bs_indices} ${ref_dir}
echo "Reference files not found. Downloading and indexing... (THIS SHOULD TAKE A WHILE)"
bash ${generate_bs_indices} ${ref_dir} > ${ref_dir}.stdout.log 2> ${ref_dir}.stderr.log
fi
......
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