Merge branch 'master' of https://github.com/soedinglab/mmseqs2

data/assembler.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 # Assembler workflow script
 checkReturnCode () { 
 	[ $? -ne 0 ] && echo "$1" && exit 1;

data/blastp.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 # Sequence search workflow script
 fail() {
     echo "Error: $1"
@@ -69,7 +69,7 @@ while [ $STEP -lt $STEPS ]; do
                 || fail "Awk step $SENS died"
         fi
 
-        if [[ ! -s "$TMP_PATH/order_step$SENS" ]]; then break; fi
+        if [ ! -s "$TMP_PATH/order_step$SENS" ]; then break; fi
 
         if notExists "$NEXTINPUT"; then
             $MMSEQS createsubdb "$TMP_PATH/order_step$SENS" "$INPUT" "$NEXTINPUT" \

data/blastpgp.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 # Iterative sequence search workflow script
 fail() {
     echo "Error: $1"

data/cascaded_clustering.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 # Clustering workflow script
 # helper functions
 checkReturnCode () { 

data/clustering.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 # Clustering workflow script
 fail() {
     echo "Error: $1"

data/linclust.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 # Clustering workflow script
 checkReturnCode () { 
 	[ $? -ne 0 ] && echo "$1" && exit 1;

data/searchtargetprofile.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 fail() {
     echo "Error: $1"
     exit 1

data/taxonomy.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 
 fail() {
     echo "Error: $1"
@@ -29,8 +29,8 @@ abspath() {
 [ ! -f "$1" ] &&  echo "$1 not found!" && exit 1;
 [ ! -f "$2" ] &&  echo "$2 not found!" && exit 1;
 [ ! -f "$3" ] &&  echo "$3 not found!" && exit 1;
-if [[ -n "${LCA_PAR}" ]]; then
-    ([[ ! -f "$4/names.dmp" ]] || [[ ! -f "$4/nodes.dmp" ]]) &&  echo "Required NCBI Taxonomy files missing!" && exit 1;
+if [ -n "${LCA_PAR}" ]; then
+    ([ ! -f "$4/names.dmp" ] || [ ! -f "$4/nodes.dmp" ]) &&  echo "Required NCBI Taxonomy files missing!" && exit 1;
     NCBI_TAXDUMP="$(abspath "$4")"
 fi
 [   -f "$5" ] &&  echo "$5 exists already!" && exit 1;
@@ -42,7 +42,7 @@ TAXON_MAPPING="$(abspath "$3")"
 RESULTS="$(abspath "$5")"
 TMP_PATH="$(abspath "$6")"
 
-if [[ ! -e "${TMP_PATH}/first" ]]; then
+if [ ! -e "${TMP_PATH}/first" ]; then
     mkdir -p "${TMP_PATH}/tmp_hsp1"
     $MMSEQS search "${INPUT}" "${TARGET}" "${TMP_PATH}/first" "${TMP_PATH}/tmp_hsp1" ${SEARCH1_PAR} \
         || fail "First search died"
@@ -51,18 +51,18 @@ fi
 LCA_SOURCE="${TMP_PATH}/first"
 
 # 2bLCA mode
-if [[ -n "${SEARCH2_PAR}" ]]; then
-    if [[ ! -e "${TMP_PATH}/top1" ]]; then
+if [ -n "${SEARCH2_PAR}" ]; then
+    if [ ! -e "${TMP_PATH}/top1" ]; then
         $MMSEQS filterdb "${TMP_PATH}/first" "${TMP_PATH}/top1" --extract-lines 1 \
             || fail "Filterdb died"
     fi
 
-    if [[ ! -e "${TMP_PATH}/aligned" ]]; then
+    if [ ! -e "${TMP_PATH}/aligned" ]; then
         $MMSEQS extractalignedregion "${TMP_PATH}/top1" "${TARGET}" "${TMP_PATH}/top1" "${TMP_PATH}/aligned" --extract-mode 2 \
             || fail "Extractalignedregion failed"
     fi
 
-    if [[ ! -e "${TMP_PATH}/round2" ]]; then
+    if [ ! -e "${TMP_PATH}/round2" ]; then
         mkdir -p "${TMP_PATH}/tmp_hsp2"
         $MMSEQS search "${TMP_PATH}/aligned" "${TARGET}" "${TMP_PATH}/round2" "${TMP_PATH}/tmp_hsp2" ${SEARCH2_PAR} \
             || fail "Second search died"
@@ -71,30 +71,30 @@ if [[ -n "${SEARCH2_PAR}" ]]; then
     # Concat top hit from first search with all the results from second search
     # We can use filterdb --beats-first to filter out all entries from second search that
     # do not reach the evalue of the top 1 hit
-    if [[ ! -e "${TMP_PATH}/merged" ]]; then
+    if [ ! -e "${TMP_PATH}/merged" ]; then
         $MMSEQS mergedbs "${TMP_PATH}/top1" "${TMP_PATH}/merged" "${TMP_PATH}/top1" "${TMP_PATH}/round2" \
             || fail "Mergedbs died"
     fi
 
-    if [[ ! -e "${TMP_PATH}/2b_ali" ]]; then
+    if [ ! -e "${TMP_PATH}/2b_ali" ]; then
         $MMSEQS filterdb "${TMP_PATH}/merged" "${TMP_PATH}/2b_ali" --beats-first --filter-column 4 --comparison-operator le \
             || fail "First filterdb died"
     fi
 
     LCA_SOURCE="${TMP_PATH}/2b_ali"
 fi
 
-if [[ ! -e "${TMP_PATH}/mapping" ]]; then
+if [ ! -e "${TMP_PATH}/mapping" ]; then
     $MMSEQS filterdb "${LCA_SOURCE}" "${TMP_PATH}/mapping" --filter-column 1 --mapping-file "${TAXON_MAPPING}" \
         || fail "Second filterdb died"
 fi
 
-if [[ ! -e "${TMP_PATH}/taxa" ]]; then
+if [ ! -e "${TMP_PATH}/taxa" ]; then
     $MMSEQS filterdb "${TMP_PATH}/mapping" "${TMP_PATH}/taxa" --filter-column 1 --trim-to-one-column \
         || fail "Third filterdb died"
 fi
 
-if [[ -n "${LCA_PAR}" ]]; then
+if [ -n "${LCA_PAR}" ]; then
     $MMSEQS lca "${TMP_PATH}/taxa" "${NCBI_TAXDUMP}" "${RESULTS}" ${LCA_PAR} \
         || fail "Lca died"
 else
@@ -108,13 +108,13 @@ if [ -n "${REMOVE_TMP}" ]; then
     rm -rf "${TMP_PATH}/tmp_hsp2"
     rm -f "${TMP_PATH}/first" "${TMP_PATH}/first.index"
 
-    if [[ -n "${SEARCH2_PAR}" ]]; then
+    if [ -n "${SEARCH2_PAR}" ]; then
         rm -f "${TMP_PATH}/top1" "${TMP_PATH}/top1.index"
         rm -f "${TMP_PATH}/aligned" "${TMP_PATH}/aligned.index" "${TMP_PATH}/round2" "${TMP_PATH}/round2.index"
         rm -f "${TMP_PATH}/merged" "${TMP_PATH}/merged.index" "${TMP_PATH}/2b_ali" "${TMP_PATH}/2b_ali.index"
     fi
 
-    if [[ -n "${LCA_PAR}" ]]; then
+    if [ -n "${LCA_PAR}" ]; then
         rm -f "${TMP_PATH}/mapping" "${TMP_PATH}/mapping.index" "${TMP_PATH}/taxa" "${TMP_PATH}/taxa.index"
     else
         rm -f "${TMP_PATH}/mapping" "${TMP_PATH}/mapping.index"