Merge pull request #51 from CALeDNA/develop

update tronko-build.sh

Dockerfile

@@ -7,12 +7,16 @@ WORKDIR /app
 RUN ulimit -d unlimited
 
 RUN apt-get update && apt-get upgrade -yy && apt-get install -yy build-essential software-properties-common \ 
-    apt-transport-https libz-dev npm cmake parallel python3-openstackclient jq awscli unzip pandoc \ 
+    apt-transport-https libz-dev npm cmake parallel python3-openstackclient jq unzip pandoc \ 
     curl wget git libssl-dev libcurl4-openssl-dev libxml2-dev -y && \
     npm i nugget -g && \
     wget -P /tmp/ "https://repo.anaconda.com/miniconda/Miniconda3-py38_4.12.0-Linux-x86_64.sh" && \
     bash "/tmp/Miniconda3-py38_4.12.0-Linux-x86_64.sh" -b -p /usr/local/miniconda
 
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" \
+    unzip awscliv2.zip \
+    ./aws/install
+
 COPY env.yml /app/env.yml
 ADD bin /usr/local/crux_bin
 

tronko/build/tronko_build.sh

@@ -4,14 +4,12 @@ set -o allexport
 export AWS_MAX_ATTEMPTS=3
 
 PARTITION_NUMBER=0
-while getopts "i:p:b:" opt; do
+while getopts "i:p:" opt; do
     case $opt in
         i) RUNID="$OPTARG"
         ;;
         p) PRIMER="$OPTARG"
         ;;
-        b) PARTITION_NUMBER="$OPTARG"
-        ;;
     esac
 done
 
@@ -33,6 +31,14 @@ partitions=$(ls ${newick}/*txt | wc -l)
 # sync down tronko output
 aws s3 sync s3://$BUCKET/CruxV2/$RUNID/$PRIMER/tronko $outdir --no-progress --endpoint-url https://js2.jetstream-cloud.org:8001/
 
+# Calculate b (PARTITION_NUMBER)
+for i in {9999..999999}; do
+    if ! [[ -e "partition${i}.fasta" && -e "partition${i}_MSA.fasta" ]]; then
+        echo "The first number without both fasta files is: ${i}"
+        PARTITION_NUMBER=$i
+        break
+    fi
+done
 
 if (( $partitions > 1 ))
 then