Commit c643f161 authored by Jarunan Panyasantisuk's avatar Jarunan Panyasantisuk
Browse files

prevent end of line bug

parent ed318093
......@@ -83,10 +83,10 @@ echo " Number of sequences: $((n_lines/2))"
# If n_lines > 2 => multiple protein sequences => multimer
if (( "$n_lines" <= 2 )); then
echo " Protein type: monomer"
OPTIONS="--pdb70_database_path=\$DATA_DIR/pdb70/pdb70 \\ "
OPTIONS="--pdb70_database_path=\$DATA_DIR/pdb70/pdb70 "
elif (( "$n_lines" > 2 )); then
echo " Protein type: multimer"
OPTIONS="--model_preset=multimer --pdb_seqres_database_path=\$DATA_DIR/pdb_seqres/pdb_seqres.txt --uniprot_database_path=$DATA_DIR/uniprot/uniprot.fasta \\ "
OPTIONS="--model_preset=multimer --pdb_seqres_database_path=\$DATA_DIR/pdb_seqres/pdb_seqres.txt --uniprot_database_path=$DATA_DIR/uniprot/uniprot.fasta"
fi
# Determine the sequence length
......@@ -200,8 +200,8 @@ python /cluster/apps/nss/alphafold/alphafold-2.1.1/run_alphafold.py \\
--mgnify_database_path=\$DATA_DIR/mgnify/mgy_clusters_2018_12.fa \\
--template_mmcif_dir=\$DATA_DIR/pdb_mmcif/mmcif_files \\
--obsolete_pdbs_path=\$DATA_DIR/pdb_mmcif/obsolete.dat \\
--fasta_paths=$FASTAFILE \\
$OPTIONS
--fasta_paths=$FASTAFILE
mkdir -p output/$PROTEIN
rsync -av \$TMPDIR/output/$PROTEIN ./output/$PROTEIN
......
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