miga-base 0.2.6.4 → 0.2.6.5

data/scripts/assembly.bash

@@ -1,53 +1,53 @@
 #!/bin/bash
-# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="assembly"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
+# shellcheck source=scripts/miga.bash
 source "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/05.assembly"
 
-b=$DATASET
-
 # Initialize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.start"
+miga date > "$DATASET.start"
 
 # Interpose (if needed)
 TF="../04.trimmed_fasta"
-if [[ -s $TF/$DATASET.1.fasta \
-      && -s $TF/$DATASET.2.fasta \
-      && ! -s $TF/$DATASET.CoupledReads.fa ]] ; then
-  FastA.interpose.pl $TF/$DATASET.CoupledReads.fa $TF/$DATASET.[12].fasta
-  gzip -9 -f $TF/$DATASET.1.fasta
-  gzip -9 -f $TF/$DATASET.2.fasta
+if [[ -s "$TF/$DATASET.1.fasta" \
+      && -s "$TF/$DATASET.2.fasta" \
+      && ! -s "$TF/$DATASET.CoupledReads.fa" ]] ; then
+  FastA.interpose.pl "$TF/$DATASET.CoupledReads.fa" "$TF/$DATASET".[12].fasta
+  gzip -9 -f "$TF/$DATASET.1.fasta"
+  gzip -9 -f "$TF/$DATASET.2.fasta"
   miga add_result -P "$PROJECT" -D "$DATASET" -r trimmed_fasta
 fi
 
 # Assemble
 FA="$TF/$DATASET.CoupledReads.fa"
-[[ -e $FA ]] || FA="$FA.gz"
-[[ -e $FA ]] || FA="../04.trimmed_fasta/$DATASET.SingleReads.fa"
-[[ -e $FA ]] || FA="$FA.gz"
+[[ -e "$FA" ]] || FA="$FA.gz"
+[[ -e "$FA" ]] || FA="../04.trimmed_fasta/$DATASET.SingleReads.fa"
+[[ -e "$FA" ]] || FA="$FA.gz"
 RD="r"
 [[ $FA == *.SingleReads.fa* ]] && RD="l"
 idba_ud --pre_correction -$RD "$FA" -o "$DATASET" --num_threads "$CORES" || true
-[[ -s $DATASET/contig.fa ]] || exit 1
+[[ -s "$DATASET/contig.fa" ]] || exit 1
 
 # Clean
-cd $DATASET
-rm kmer graph-*.fa align-* local-contig-*.fa contig-*.fa
-cd ..
+(
+  cd "$DATASET"
+  rm kmer graph-*.fa align-* local-contig-*.fa contig-*.fa
+)
 
 # Extract
-if [[ -s $DATASET/scaffold.fa ]] ; then
-   ln -s $DATASET/scaffold.fa $DATASET.AllContigs.fna
+if [[ -s "$DATASET/scaffold.fa" ]] ; then
+  ln -s "$DATASET/scaffold.fa" "$DATASET.AllContigs.fna"
 else
-   ln -s $DATASET/contig.fa $DATASET.AllContigs.fna
+  ln -s "$DATASET/contig.fa" "$DATASET.AllContigs.fna"
 fi
-FastA.length.pl $DATASET.AllContigs.fna | awk '$2>=1000{print $1}' \
-   | FastA.filter.pl /dev/stdin $DATASET.AllContigs.fna \
-   > $DATASET.LargeContigs.fna
+FastA.length.pl "$DATASET.AllContigs.fna" | awk '$2>=1000{print $1}' \
+  | FastA.filter.pl /dev/stdin "$DATASET.AllContigs.fna" \
+  > "$DATASET.LargeContigs.fna"
 
 # Finalize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
+miga date > "$DATASET.done"
 miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/cds.bash

@@ -1,46 +1,38 @@
 #!/bin/bash
-# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="cds"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
+# shellcheck source=scripts/miga.bash
 source "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/06.cds"
 
 # Initialize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.start"
-GM=$(dirname -- $(which gmhmmp))
+miga date > "$DATASET.start"
 
-# Register key
-if [[ ! -e .gm_key ]] ; then
-   if [[ -e "$GM/gm_key" ]] ; then
-      cp "$GM/gm_key" ".gm_key"
-   elif [[ -e "$GM/gm_key_64" ]] ; then
-      cp "$GM/gm_key_64" ".gm_key"
-   elif [[ -e "$GM/gm_key_32" ]] ; then
-      cp "$GM/gm_key_32" ".gm_key"
-   elif [[ -e "$GM/.gm_key" ]] ; then
-      cp "$GM/.gm_key" ".gm_key"
-   elif [[ -e "$HOME/.gm_key" ]] ; then
-      cp "$HOME/.gm_key" .
-   else
-      echo "Impossible to find MetaGeneMark key, please register your copy" \
-	 "and place the key in '$GM/gm_key'." >&2
-      exit 1
-   fi
-fi
+# Run Prodigal
+TYPE=$(miga list_datasets -P "$PROJECT" -D "$DATASET" \
+   --metadata "type" | awk '{print $2}')
+case "$TYPE" in
+  metagenome|virome) PROCEDURE=meta ;;
+  *) PROCEDURE=single ;;
+esac
+prodigal -a "$DATASET.faa" -d "$DATASET.fna" -f gff -o "$DATASET.gff3" \
+  -p $PROCEDURE -q -i "../05.assembly/$DATASET.LargeContigs.fna"
 
-# Run MetaGeneMark
-gmhmmp -a -d -m "$GM/MetaGeneMark_v1.mod" -f G -o "$DATASET.gff2" \
-   "../05.assembly/$DATASET.LargeContigs.fna"
-
-# Extract
-perl "$GM/aa_from_gff.pl" < "$DATASET.gff2" > "$DATASET.faa"
-perl "$GM/nt_from_gff.pl" < "$DATASET.gff2" > "$DATASET.fna"
+# Clean Prodigal noisy deflines
+for i in faa fna ; do
+  perl -pe 's/>.*ID=([^;]+);.*/>gene_$1/' "$DATASET.$i" > "$DATASET.$i.t"
+  mv "$DATASET.$i.t" "$DATASET.$i"
+done
+perl -pe 's/ID=([0-9]+_[0-9]+);/ID=gene_$1;/' "$DATASET.gff3" \
+  > "$DATASET.gff3.t"
+mv "$DATASET.gff3.t" "$DATASET.gff3"
 
 # Gzip
-gzip -9 -f "$DATASET.gff2"
+gzip -9 -f "$DATASET.gff3"
 
 # Finalize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
+miga date > "$DATASET.done"
 miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/clade_finding.bash

@@ -4,11 +4,12 @@ set -e
 SCRIPT="clade_finding"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
+# shellcheck source=scripts/miga.bash
 source "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/10.clades/01.find"
 
 # Initialize
-date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.start"
+miga date > "miga-project.start"
 
 # Markov-cluster genomes by ANI
 gunzip -c ../../09.distances/03.ani/miga-project.txt.gz | tail -n+2 \
@@ -30,9 +31,9 @@ cat miga-project.ani95-clades | tail -n +2 | tr "," "\\t" | awk 'NF >= 5' \
 
 # Run R code (except in projects type clade)
 if [[ $(miga project_info -P "$PROJECT" -m type) != "clade" ]] ; then
-  $MIGA/utils/subclades.R \
+  "$MIGA/utils/subclades.R" \
     ../../09.distances/02.aai/miga-project.txt.gz \
-    miga-project $CORES
+    miga-project "$CORES"
   mv miga-project.nwk miga-project.aai.nwk
   
   # Compile
@@ -42,5 +43,5 @@ if [[ $(miga project_info -P "$PROJECT" -m type) != "clade" ]] ; then
 fi
 
 # Finalize
-date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.done"
+miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT"

data/scripts/distances.bash

@@ -1,32 +1,36 @@
 #!/bin/bash
-# Available variables: $PROJECT, $DATASET, $RUNTYPE, $MIGA, $CORES
+# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="distances"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
+# shellcheck source=scripts/miga.bash
 source "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/09.distances"
 
 # Initialize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.start"
+miga date > "$DATASET.start"
 TMPDIR=$(mktemp -d /tmp/MiGA.XXXXXXXXXXXX)
-trap "rm -rf $TMPDIR; exit" SIGHUP SIGINT SIGTERM
+trap "rm -rf '$TMPDIR'; exit" SIGHUP SIGINT SIGTERM
 
 # Check type of dataset
 NOMULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --no-multi \
-   | wc -l | awk '{print $1}')
+  | wc -l | awk '{print $1}')
 REF=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --ref \
-   | wc -l | awk '{print $1}')
+  | wc -l | awk '{print $1}')
 
 # Call submodules
+# shellcheck source=scripts/_distances_functions.bash
 source "$MIGA/scripts/_distances_functions.bash"
 if [[ "$NOMULTI" -eq "1" && "$REF" -eq "1" ]] ; then
-   source "$MIGA/scripts/_distances_ref_nomulti.bash"
+  # shellcheck source=scripts/_distances_ref_nomulti.bash
+  source "$MIGA/scripts/_distances_ref_nomulti.bash"
 elif [[ "$NOMULTI" -eq "1" ]] ; then
-   source "$MIGA/scripts/_distances_noref_nomulti.bash"
+  # shellcheck source=scripts/_distances_noref_nomulti.bash
+  source "$MIGA/scripts/_distances_noref_nomulti.bash"
 fi
 
 # Finalize
-rm -R $TMPDIR
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
+rm -R "$TMPDIR"
+miga date > "$DATASET.done"
 miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/essential_genes.bash

@@ -1,21 +1,22 @@
 #!/bin/bash
-# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
+# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="essential_genes"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
+# shellcheck source=scripts/miga.bash
 source "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/07.annotation/01.function/01.essential"
 
 # Initialize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.start"
+miga date > "$DATASET.start"
 FAA="../../../06.cds/$DATASET.faa"
 
 # Check if there are any proteins
 if [[ ! -s $FAA ]] ; then
   echo Empty protein set, bypassing essential genes
   rm "$DATASET.start"
-  miga create_dataset -P "$PROJECT" -D $DATASET \
+  miga create_dataset -P "$PROJECT" -D "$DATASET" \
     -m run_essential_genes=false --update
   exit 0
 fi
@@ -24,17 +25,17 @@ fi
 [[ -d "$DATASET.ess" ]] && rm -R "$DATASET.ess"
 mkdir "$DATASET.ess"
 TYPE=$(miga list_datasets -P "$PROJECT" -D "$DATASET" \
-   --metadata "type" | awk '{print $2}')
+  --metadata "type" | awk '{print $2}')
 if [[ "$TYPE" == "metagenome" || "$TYPE" == "virome" ]] ; then
-   HMM.essential.rb -i "$FAA" -o "$DATASET.ess.faa" \
-      -m "$DATASET.ess/" -t "$CORES" -r "$DATASET" --metagenome \
-      > "$DATASET.ess/log"
+  HMM.essential.rb -i "$FAA" -o "$DATASET.ess.faa" \
+    -m "$DATASET.ess/" -t "$CORES" -r "$DATASET" --metagenome \
+    > "$DATASET.ess/log"
 else
-   HMM.essential.rb -i "$FAA" -o "$DATASET.ess.faa" \
-      -m "$DATASET.ess/" -t "$CORES" -r "$DATASET" \
-      > "$DATASET.ess/log"
+  HMM.essential.rb -i "$FAA" -o "$DATASET.ess.faa" \
+    -m "$DATASET.ess/" -t "$CORES" -r "$DATASET" \
+    > "$DATASET.ess/log"
 fi
 
 # Finalize
-date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
+miga date > "$DATASET.done"
 miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/haai_distances.bash

@@ -4,11 +4,12 @@ set -e
 SCRIPT="haai_distances"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
+# shellcheck source=scripts/miga.bash
 source "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/09.distances/01.haai"
 
 # Initialize
-date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.start"
+miga date > "miga-project.start"
 
 echo -n "" > miga-project.log
 DS=$(miga list_datasets -P "$PROJECT" --ref --no-multi)
@@ -39,5 +40,5 @@ if(sum(haai[,'a'] != haai[,'b']) > 0){
 gzip -9 -f miga-project.txt
 
 # Finalize
-date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.done"
+miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT"

data/scripts/init.bash

@@ -3,39 +3,40 @@ set -e
 
 #=======[ Functions ]
 function ask_user {
-   local question=$1
-   local default=$2
-   echo $question >&2
-   echo -n "  [$default] > " >&2
-   read user_answer
-   user_answer=${user_answer:-$default}
-   echo -n "$user_answer"
+  local question=$1
+  local default=$2
+  echo "$question" >&2
+  echo -n "  [$default] > " >&2
+  read -r user_answer
+  user_answer=${user_answer:-$default}
+  echo -n "$user_answer"
 }
 
 function check_req {
-   local bin=$1
-   local default=$(dirname "$(which "$bin")")
-   user_answer=$(ask_user "Where can I find $2 ($3)? $4" "$default")
-   if [[ -x "$user_answer/$bin" ]] ; then
-      export PATH="$PATH:$user_answer"
-      echo "MIGA_PATH=\"$user_answer:\$MIGA_PATH\" # $2" >> "$HOME/.miga_rc"
-   else
-      echo "Cannot find $2 at '$user_answer/$bin'. Aborting..." >&2
-      exit 1
-   fi
+  local bin=$1
+  local default
+  default=$(dirname "$(which "$bin")")
+  user_answer=$(ask_user "Where can I find $2 ($3)? $4" "$default")
+  if [[ -x "$user_answer/$bin" ]] ; then
+    export PATH="$PATH:$user_answer"
+    echo "MIGA_PATH=\"$user_answer:\$MIGA_PATH\" # $2" >> "$HOME/.miga_rc"
+  else
+    echo "Cannot find $2 at '$user_answer/$bin'. Aborting..." >&2
+    exit 1
+  fi
 }
 
 function check_rlib {
-   local rlib=$1
-   gotit=$(echo "if(require($rlib)) cat('GOT','IT')" | R --vanilla -q 2>&1 \
-      | grep "GOT IT" | wc -l | awk '{print $1}')
-   [[ "$gotit" == "1" ]]
+  local rlib=$1
+  gotit=$(echo "if(require($rlib)) cat('GOT','IT')" | R --vanilla -q 2>&1 \
+    | grep -c "GOT IT")
+  [[ "$gotit" == "1" ]]
 }
 
 function check_gem {
-   local gem=$1
-   gotit=$(echo "require '$gem'" | ruby 2>/dev/null && echo 1)
-   [[ "$gotit" == "1" ]]
+  local gem=$1
+  gotit=$(echo "require '$gem'" | ruby 2>/dev/null && echo 1)
+  [[ "$gotit" == "1" ]]
 }
 
 #=======[ Main ]
@@ -49,31 +50,32 @@ make sure you have all the requirements for MiGA Daemons.
 " >&2
 
 if [[ "$(ask_user "Would you like to see all the requirements before starting? (yes / no)" "no")" == "yes" ]] ; then
-   echo "" >&2
-   cat "$MIGA/utils/requirements.txt" >&2
-   echo "" >&2
+  echo "" >&2
+  cat "$MIGA/utils/requirements.txt" >&2
+  echo "" >&2
 fi
 
 if [[ -e "$HOME/.miga_rc" ]] ; then
-   case "$(ask_user "I found a previous configuration. Do you want to load the defaults within? (yes / no / cancel)" "yes")" in
-      yes)
-	 source "$HOME/.miga_rc"
-	 if [[ "$MIGA_CONFIG_DATE" == "" ]] ; then
-	    echo "  Loaded incomplete configuration" >&2
-	 else
-	    echo "  Loaded configuration from $MIGA_CONFIG_DATE" >&2
-	 fi
-	 ;;
-      no)
-	 rm "$HOME/.miga_rc"
-	 ;;
-      cancel)
-	 exit 0
-	 ;;
-      *)
-	 echo "Cannot understand your answer, please use 'yes', 'no', or 'cancel'. Aborting..." >&2
-	 exit 1
-   esac
+  case "$(ask_user "I found a previous configuration. Do you want to load the defaults within? (yes / no / cancel)" "yes")" in
+    yes)
+      # shellcheck source=/dev/null
+      source "$HOME/.miga_rc"
+      if [[ "$MIGA_CONFIG_DATE" == "" ]] ; then
+        echo "  Loaded incomplete configuration" >&2
+      else
+        echo "  Loaded configuration from $MIGA_CONFIG_DATE" >&2
+      fi
+      ;;
+    no)
+      rm "$HOME/.miga_rc"
+      ;;
+    cancel)
+      exit 0
+      ;;
+    *)
+      echo "Cannot understand your answer, please use 'yes', 'no', or 'cancel'. Aborting..." >&2
+      exit 1
+  esac
 fi
 
 echo "#!/bin/bash
@@ -83,10 +85,11 @@ echo "#!/bin/bash
 # Check Software requirements
 MIGA_STARTUP=$(ask_user "Is there a script I need to load at startup? (no / path to the script to load)" "$MIGA_STARTUP")
 if [[ "$MIGA_STARTUP" != "no" ]] ; then
-   echo "MIGA_STARTUP='$MIGA_STARTUP'
+  echo "MIGA_STARTUP='$MIGA_STARTUP'
 source \"\$MIGA_STARTUP\"
 " >> "$HOME/.miga_rc";
-   source "$MIGA_STARTUP";
+  # shellcheck source=/dev/null
+  source "$MIGA_STARTUP";
 fi
 echo "
 Looking for Software requirements:" >&2
@@ -94,11 +97,11 @@ reqs=$(tail -n+3 "$MIGA/utils/requirements.txt" | perl -pe 's/\t+/\t/g')
 IFS_BU=$IFS
 IFS=$'\n'
 for ln in $reqs ; do
-   rname=$(echo "$ln" | awk -F'\t' '{print $1}')
-   rtest=$(echo "$ln" | awk -F'\t' '{print $2}')
-   rwebs=$(echo "$ln" | awk -F'\t' '{print $3}')
-   rhint=$(echo "$ln" | awk -F'\t' '{print $4}')
-   check_req "$rtest" "$rname" "$rwebs" "$rhint"
+  rname=$(echo "$ln" | awk -F'\t' '{print $1}')
+  rtest=$(echo "$ln" | awk -F'\t' '{print $2}')
+  rwebs=$(echo "$ln" | awk -F'\t' '{print $3}')
+  rhint=$(echo "$ln" | awk -F'\t' '{print $4}')
+  check_req "$rtest" "$rname" "$rwebs" "$rhint"
 done
 IFS=$IFS_BU
 echo "export PATH=\$MIGA_PATH\$PATH" >> "$HOME/.miga_rc"
@@ -108,11 +111,11 @@ echo "
 Looking for R packages:" >&2
 RLIBS="enveomics.R ape phangorn phytools ggdendro ggplot2 gridExtra cluster dendextend vegan scatterplot3d"
 for lib in $RLIBS ; do
-   if ! check_rlib $lib ; then
-      echo "+ Installing $lib" >&2
-      echo "install.packages('$lib', repos='http://cran.rstudio.com/')" \
-	 | R --vanilla -q
-   fi
+  if ! check_rlib "$lib" ; then
+    echo "+ Installing $lib" >&2
+    echo "install.packages('$lib', repos='http://cran.rstudio.com/')" \
+      | R --vanilla -q
+  fi
 done
 
 # Check for ruby gems
@@ -120,36 +123,25 @@ echo "
 Looking for Ruby gems:" >&2
 GEMS="rest-client sqlite3 daemons json"
 for gem in $GEMS ; do
-   if ! check_gem $gem ; then
-      echo "+ Installing $gem (user-only)" >&2
-      gem install --user $gem
-   fi
+  if ! check_gem "$gem" ; then
+    echo "+ Installing $gem (user-only)" >&2
+    gem install --user "$gem"
+  fi
 done
 
 # Check for other files
 echo "
 Looking for additional files:
-+ MetaGeneMark license key" >&2
-GM=$(dirname -- $(which gmhmmp))
-if [[ ! -e "$GM/gm_key" && ! -e "$GM/gm_key_64" && ! -e "$GM/gm_key_32" && ! -e "$GM/.gm_key" && ! -e "$HOME/.gm_key" ]] ; then
-   echo "Cannot find it, please place your license key in '$GM/gm_key'. Aborting..." >&2
-   exit 1
-fi
-echo "+ MetaGeneMark scripts" >&2
-if [[ ! -e "$GM/aa_from_gff.pl" || ! -e "$GM/nt_from_gff.pl" ]] ; then
-   echo "Cannot find it, please place aa_from_gff.pl and nt_from_gff.pl in '$GM/'. Aborting..." >&2
-   exit 1
-fi
-echo "+ MyTaxa scores database" >&2
-MT=$(dirname -- $(which MyTaxa))
++ MyTaxa scores database" >&2
+MT=$(dirname -- "$(which MyTaxa)")
 if [[ ! -d "$MT/db" ]] ; then
-   echo "Cannot find it, please execute 'python $MT/utils/download_db.py'. Aborting..." >&2
-   exit 1
+  echo "Cannot find it, please execute 'python $MT/utils/download_db.py'. Aborting..." >&2
+  exit 1
 fi
 echo "+ MyTaxa DIAMOND database" >&2
 if [[ ! -e "$MT/AllGenomes.faa.dmnd" ]] ; then
-   echo "Cannot find it, please download 'http://enve-omics.ce.gatech.edu/data/public_mytaxa/AllGenomes.faa.dmnd' into '$MT'. Aborting..." >&2
-   exit 1
+  echo "Cannot find it, please download 'http://enve-omics.ce.gatech.edu/data/public_mytaxa/AllGenomes.faa.dmnd' into '$MT'. Aborting..." >&2
+  exit 1
 fi
 
 # Configure daemon
@@ -157,34 +149,34 @@ echo "
 Default daemon configuration:" >&2
 dtype=$(ask_user "Please select the type of daemon you want to setup (bash / qsub / msub)", "bash")
 case "$dtype" in
-   bash)
-      dlatency=$(ask_user "For how long should I sleep? (# in seconds)" "30")
-      dmaxjobs=$(ask_user "How many jobs can I launch at once?" "6")
-      dppn=$(ask_user "How many CPUs can I use per job?" "2")
-      echo "Setting up internal daemon defaults, if you don't understand this just leave default values:" >&2
-      dcmd=$(ask_user "How should I launch tasks? Use %1\$s for script path, %2\$s for variables, %3\$d for CPUs, %4\$s for log file, and %5\$s for task name." "%2\$s '%1\$s' > '%4\$s' 2>&1")
-      dvar=$(ask_user "How should I pass variables? Use %1\$s for keys and %2\$s for values." "%1\$s=%2\$s")
-      dsep=$(ask_user "What should I use to separate variables?" " ")
-      dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for PID, output should be 1 for running and 0 for non-running." "ps -p '%1\$s'|tail -n+2|wc -l|awk '{print \$1}'")
-      ;;
-   [qm]sub)
-      dqueue=$(ask_user "What's the name of the queue I should use?" "")
-      dlatency=$(ask_user "How long should I sleep? (# in seconds)" "150")
-      dmaxjobs=$(ask_user "How many jobs can I launch at once?" "300")
-      dppn=$(ask_user "How many CPUs can I use per job?" "4")
-      echo "Setting up internal daemon defaults, if you don't understand this just leave default values:" >&2
-      dcmd=$(ask_user "How should I launch tasks? Use %1\$s for script path, %2\$s for variables, and %3\$d for CPUs, %4\$d for log file, and %5\$s for task name." \
-	 "$dtype -q '$dqueue' -v '%2\$s' -l nodes=1:ppn=%3\$d %1\$s -j oe -o '%4\$s' -N '%5\$s' | grep .")
-      dvar=$(ask_user "How should I pass variables? Use %1\$s for keys and %2\$s for values." "%1\$s=%2\$s")
-      dsep=$(ask_user "What should I use to separate variables?" ",")
-      if [[ "$dtype" == "qsub" ]] ; then
-	 dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for job id, output should be 1 for running and 0 for non-running." \
-	    "qstat -f '%1\$s'|grep ' job_state ='|perl -pe 's/.*= //'|grep '[^C]'|tail -n1|wc -l|awk '{print \$1}'")
-      else
-	 dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for job id, output should be 1 for running and 0 for non-running." \
-	    "checkjob '%1\$s'|grep '^State:'|perl -pe 's/.*: //'|grep 'Deferred\\|Hold\\|Idle\\|Starting\\|Running\\|Blocked'|tail -n1|wc -l|awk '{print \$1}'")
-      fi
-      ;;
+  bash)
+    dlatency=$(ask_user "For how long should I sleep? (# in seconds)" "30")
+    dmaxjobs=$(ask_user "How many jobs can I launch at once?" "6")
+    dppn=$(ask_user "How many CPUs can I use per job?" "2")
+    echo "Setting up internal daemon defaults, if you don't understand this just leave default values:" >&2
+    dcmd=$(ask_user "How should I launch tasks? Use %1\$s for script path, %2\$s for variables, %3\$d for CPUs, %4\$s for log file, and %5\$s for task name." "%2\$s '%1\$s' > '%4\$s' 2>&1")
+    dvar=$(ask_user "How should I pass variables? Use %1\$s for keys and %2\$s for values." "%1\$s=%2\$s")
+    dsep=$(ask_user "What should I use to separate variables?" " ")
+    dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for PID, output should be 1 for running and 0 for non-running." "ps -p '%1\$s'|tail -n+2|wc -l|awk '{print \$1}'")
+    ;;
+  [qm]sub)
+    dqueue=$(ask_user "What's the name of the queue I should use?" "")
+    dlatency=$(ask_user "How long should I sleep? (# in seconds)" "150")
+    dmaxjobs=$(ask_user "How many jobs can I launch at once?" "300")
+    dppn=$(ask_user "How many CPUs can I use per job?" "4")
+    echo "Setting up internal daemon defaults, if you don't understand this just leave default values:" >&2
+    dcmd=$(ask_user "How should I launch tasks? Use %1\$s for script path, %2\$s for variables, and %3\$d for CPUs, %4\$d for log file, and %5\$s for task name." \
+       "$dtype -q '$dqueue' -v '%2\$s' -l nodes=1:ppn=%3\$d %1\$s -j oe -o '%4\$s' -N '%5\$s' | grep .")
+    dvar=$(ask_user "How should I pass variables? Use %1\$s for keys and %2\$s for values." "%1\$s=%2\$s")
+    dsep=$(ask_user "What should I use to separate variables?" ",")
+    if [[ "$dtype" == "qsub" ]] ; then
+      dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for job id, output should be 1 for running and 0 for non-running." \
+        "qstat -f '%1\$s'|grep ' job_state ='|perl -pe 's/.*= //'|grep '[^C]'|tail -n1|wc -l|awk '{print \$1}'")
+    else
+      dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for job id, output should be 1 for running and 0 for non-running." \
+        "checkjob '%1\$s'|grep '^State:'|perl -pe 's/.*: //'|grep 'Deferred\\|Hold\\|Idle\\|Starting\\|Running\\|Blocked'|tail -n1|wc -l|awk '{print \$1}'")
+    fi
+    ;;
    *)
 esac
 echo "{
@@ -198,7 +190,7 @@ echo "{
    \"latency\": $dlatency,
    \"maxjobs\": $dmaxjobs,
    \"ppn\"    : $dppn
-}" > $HOME/.miga_daemon.json
+}" > "$HOME/.miga_daemon.json"
 
 # Confirm configuration
 echo "

data/scripts/miga.bash

@@ -1,14 +1,16 @@
 #!/bin/bash
 set -e
 #MIGA=${MIGA:-$(cd "$(dirname "$0")/.."; pwd)}
+# shellcheck source=/dev/null
 source "$HOME/.miga_rc"
 export PATH="$MIGA/bin:$PATH"
-SCRIPT=${SCRIPT:-$(basename $0 .bash)}
+SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
 
 function exists { [[ -e "$1" ]] ; }
-function fx_exists { [[ $(type -t $1) == "function" ]] ; }
+function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
 
 for i in $(miga plugins -P "$PROJECT") ; do
+  # shellcheck source=/dev/null
   source "$i/scripts-plugin.bash"
 done