update qc img

CALeDNA · Feb 20, 2024 · 8dd9a10 · 8dd9a10
1 parent ffe0f6b
commit 8dd9a10
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/tronko/assign/Dockerfile b/tronko/assign/Dockerfile
@@ -5,7 +5,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 WORKDIR /mnt
 
 RUN apt-get update && apt-get upgrade -yy && apt-get install -yy build-essential software-properties-common awscli \ 
-    curl wget git libssl-dev libcurl4-openssl-dev libxml2-dev r-base-core pandoc -y && \
+    curl wget git libssl-dev libcurl4-openssl-dev libxml2-dev r-base-core pandoc jq -y && \
     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
 

diff --git a/tronko/assign/qc.sh b/tronko/assign/qc.sh
@@ -40,11 +40,11 @@ echo $secret_json | jq -r 'to_entries|map("export \(.key)=\(.value|tostring)")|.
 source export_vars.sh && rm export_vars.sh
 
 # download samples
-aws s3 sync s3://$S3_BUCKET/projects/$PROJECTID/samples $PROJECTID-$PRIMER/samples --no-progress --endpoint-url $S3_ENDPOINT
+aws s3 sync s3://$S3_BUCKET/projects/$PROJECTID/samples $PROJECTID-$PRIMER/samples --no-progress
 
 
 # download primer info
-aws s3 sync s3://$S3_BUCKET/projects/$PROJECTID/QC $PROJECTID-$PRIMER/ --exclude "*/*" --no-progress --endpoint-url $S3_ENDPOINT
+aws s3 sync s3://$S3_BUCKET/projects/$PROJECTID/QC $PROJECTID-$PRIMER/ --exclude "*/*" --no-progress
 
 # Set creds for js2 to download old QC if they exist
 switchAWSCreds $JS2_ACCESS_KEY_ID $JS2_SECRET_ACCESS_KEY $JS2_DEFAULT_REGION
@@ -103,7 +103,7 @@ if [ "$unpaired_R_files" -gt 0 ]; then
 fi
 
 # add tronko assign job on $PRIMER
-ben add -s $BENSERVER -c "docker run --rm -t -v ~/crux/tronko/assign:/mnt -v ~/crux/crux/vars:/vars -v /tmp:/tmp -e S3_ACCESS_KEY_ID=$S3_ACCESS_KEY_ID -e S3_SECRET_ACCESS_KEY=$S3_SECRET_ACCESS_KEY -e S3_DEFAULT_REGION=$S3_DEFAULT_REGION -e S3_BUCKET=$S3_BUCKET -e S3_ENDPOINT=$S3_ENDPOINT --name $PROJECTID-assign-$PRIMER crux /mnt/assign.sh -i $PROJECTID -r $RUNID -p $PRIMER $parameters" $PROJECTID-assign-$PRIMER -o $OUTPUT
+ben add -s $BENSERVER -c "docker run --rm -t -v ~/crux/tronko/assign:/mnt -v ~/crux/crux/vars:/vars -v /tmp:/tmp -e S3_ACCESS_KEY_ID=$S3_ACCESS_KEY_ID -e S3_SECRET_ACCESS_KEY=$S3_SECRET_ACCESS_KEY -e S3_DEFAULT_REGION=$S3_DEFAULT_REGION -e S3_BUCKET=$S3_BUCKET --name $PROJECTID-assign-$PRIMER crux /mnt/assign.sh -i $PROJECTID -r $RUNID -p $PRIMER $parameters" $PROJECTID-assign-$PRIMER -o $OUTPUT
 
 # clean up
 rm -r /mnt/$PROJECTID-$PRIMER /mnt/Anacapa