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Fix shell-escape errors

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martin-steinegger committed Mar 18, 2019
1 parent f30dfd9 commit 8d07a823eae587cd3dbec34cb0aea5f4fc240042
Showing with 4 additions and 4 deletions.
  1. +4 −4 data/assembler.sh
@@ -90,7 +90,7 @@ while [ "$STEP" -lt "$NUM_IT" ]; do
# shellcheck disable=SC2086
$RUNNER "$MMSEQS" kmermatcher "$INPUT" "${TMP_PATH}/pref_$STEP" ${KMERMATCHER_TMP} \
|| fail "Kmer matching step died"
deleteIncremental $PREV_KMER_PREF
deleteIncremental "$PREV_KMER_PREF"
touch "${TMP_PATH}/pref_$STEP.done"
PREV_KMER_PREF="${TMP_PATH}/pref_$STEP"

@@ -102,7 +102,7 @@ while [ "$STEP" -lt "$NUM_IT" ]; do
$RUNNER "$MMSEQS" rescorediagonal "$INPUT" "$INPUT" "${TMP_PATH}/pref_$STEP" "${TMP_PATH}/aln_$STEP" ${UNGAPPED_ALN_PAR} \
|| fail "Ungapped alignment step died"
touch "${TMP_PATH}/aln_$STEP.done"
deleteIncremental $PREV_ALN
deleteIncremental "$PREV_ALN"
PREV_ALN="${TMP_PATH}/aln_$STEP"
fi

@@ -122,7 +122,7 @@ while [ "$STEP" -lt "$NUM_IT" ]; do
$RUNNER "$MMSEQS" rescorediagonal "$INPUT" "$INPUT" "${TMP_PATH}/pref_$STEP" "${TMP_PATH}/aln_corrected_$STEP" ${UNGAPPED_ALN_PAR} \
|| fail "Ungapped alignment step died"
touch "${TMP_PATH}/aln_corrected_$STEP.done"
deleteIncremental $PREV_ALN
deleteIncremental "$PREV_ALN"
PREV_ALN="${TMP_PATH}/aln_corrected_$STEP"
fi
ALN="${TMP_PATH}/aln_corrected_$STEP"
@@ -135,7 +135,7 @@ while [ "$STEP" -lt "$NUM_IT" ]; do
|| fail "Assembly step died"

touch "${TMP_PATH}/assembly_$STEP.done"
deleteIncremental $PREV_ASSEMBLY
deleteIncremental "$PREV_ASSEMBLY"
PREV_ASSEMBLY="${TMP_PATH}/assembly_$STEP"
fi

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