diff --git a/README.md b/README.md
index c5c9dd3d..aaa1364d 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Daylily AWS Ephemeral Cluster Setup (0.7.155)
+# Daylily AWS Ephemeral Cluster Setup (0.7.156)
 _(0.7.155)_
 
 **beta release**
@@ -87,7 +87,6 @@ I will be assessing:
 > Would you like to lend a hand?  [contact me](mailto:john@daylilyinformatics.com)
 
 
-
 # What's It All About?
 
 ## BFAIR: Bioinformatics [FAIR](https://www.go-fair.org/fair-principles/) Principles 
@@ -251,22 +250,25 @@ You may run in any region or AZ you wish to try. This said, the majority of test
 
 
 ## Prerequisites (On Your Local Machine) 
-Local machine development has been exclusively on a mac, using the `zsh` shell (I am moving everything to bash, so there is a mix of bash and zsh at the moment. All `.` and `sourcing` that happens on your local machine expects `zsh`).
+Local machine development has been carried out exclusively on a mac using the `zsh` shell. `bash` should work as well (if you have issues with conda w/mac+bash, confirm that after miniconda install and conda init, the correct `.bashrc` and `.bash_profile` files were updated by `conda init`).
  
 _suggestion: run things in tmux or screen_
 
 Very good odds this will work on any mac and most Linux distros (ubuntu 22.04 are what the cluster nodes run). Windows, I can't say.
 
 ### System Packages
-Install with `brew` or `apt-get` ('):
-- `python3`, tested with `3.12.8`
+Install with `brew` or `apt-get`:
+- `python3`, tested with `3.11.0
 - `git`, tested with `2.46.0`
-- `jq`, tested with `jq-1.7.1`
 - `wget`, tested with `1.25.0`
 - `awscli`, tested with `2.22.4` [AWS CLI docs](https://docs.aws.amazon.com/cli/latest/userguide/install-cliv2.html)
 - `tmux` (optional, but suggested)
 - `emacs` (optional, I guess, but I'm not sure how to live without it)
 
+#### Check if your prereq's meet the min versions required
+```bash
+./bin/check_prereq_sw.sh 
+```
 
 ### AWS CLI Configuration
 #### Opt 2
@@ -323,29 +325,32 @@ git clone https://github.com/Daylily-Informatics/daylily.git  # or, if you have
 cd daylily
 ```
 
-### Miniconda
+### Install Miniconda (homebrew is not advised)
 _tested with conda version **`24.11.1`**_
 
-```bash
 Install with:
 ```bash
-source bin/install_miniconda
+./bin/install_miniconda
 ```
-- This will leave you in a terminal with conda activated, indicated by `(base)` in the terminal prompt.
+- open a new terminal/shell, and conda should be available: `conda -v`.
 
-### DAYCLI Environment
+### Install DAYCLI Environment
 _from `daylily` root dir_
 
 ```bash
-#!/bin/zsh
 
-source bin/init_daycli 
+./bin/init_daycli 
+
+conda activate DAYCLI
 
 # DAYCLI should now be active... did it work?
 colr  'did it work?' 0,100,255 255,100,0
 
 ```
-- This will leave you in a terminal with the conda DAYCLI activated, indicated by `(DAYCLI)` in the terminal prompt.
+
+- You should see:
+ 
+  > ![](docs/images/diw.png)
 
 
 <p valign="middle"><img src="docs/images/000000.png" valign="bottom" ></p>
@@ -377,17 +382,17 @@ _running in a tmux/screen session is advised as the copy may take 1-many hours_
 ```bash
 conda activate DAYCLI
 # help
-bash ./bin/create_daylily_omics_analysis_s3.sh -h
+./bin/create_daylily_omics_analysis_s3.sh -h
 
-AWS_PROFILE=<your_profile>
+export AWS_PROFILE=<your_profile>
 BUCKET_PREFIX=<your_prefix>
 REGION=us-west-2
 
 # dryrun
-bash ./bin/create_daylily_omics_analysis_s3.sh  --disable-warn --region $REGION --profile $AWS_PROFILE --bucket-prefix $BUCKET_PREFIX
+./bin/create_daylily_omics_analysis_s3.sh  --disable-warn --region $REGION --profile $AWS_PROFILE --bucket-prefix $BUCKET_PREFIX
 
 # run for real
-bash ./bin/create_daylily_omics_analysis_s3.sh  --disable-warn --region $REGION --profile $AWS_PROFILE --bucket-prefix $BUCKET_PREFIX --disable-dryrun
+./bin/create_daylily_omics_analysis_s3.sh  --disable-warn --region $REGION --profile $AWS_PROFILE --bucket-prefix $BUCKET_PREFIX --disable-dryrun
 
 ```
 
@@ -406,7 +411,7 @@ _this command will take ~5min to complete, and much longer if you expand to all
 ```bash
 
 conda activate DAYCLI
-AWS_PROFILE=daylily-service
+export AWS_PROFILE=daylily-service
 REGION=us-west-2          
 OUT_TSV=./init_daylily_cluster.tsv
 
@@ -474,14 +479,13 @@ Once you have selected an AZ && have a reference bucket ready in the region this
 
 The following script will check a variety of required resources, attempt to create some if missing and then prompt you to select various options which will all be used to create a new parallel cluster yaml config, which in turn is used to create the cluster via `StackFormation`. [The template yaml file can be checked out here](config/day_cluster/prod_cluster.yaml).
 
-```zsh
-#!/bin/zsh
-AWS_PROFILE=daylily-service
+```bash
+export AWS_PROFILE=daylily-service
 REGION_AZ=us-west-2c
-source bin/daylily-create-ephemeral-cluster --region-az $REGION_AZ --profile $AWS_PROFILE
+./bin/daylily-create-ephemeral-cluster --region-az $REGION_AZ --profile $AWS_PROFILE
 
 # And to bypass the non-critical warnings (which is fine, not all can be resolved )
-source bin/daylily-create-ephemeral-cluster --region-az $REGION_AZ --profile $AWS_PROFILE --pass-on-warn # If you created an inline policy with a name other than daylily-service-cluster-policy, you will need to acknowledge the warning to proceed (assuming the policy permissions were granted other ways)
+./bin/daylily-create-ephemeral-cluster --region-az $REGION_AZ --profile $AWS_PROFILE --pass-on-warn # If you created an inline policy with a name other than daylily-service-cluster-policy, you will need to acknowledge the warning to proceed (assuming the policy permissions were granted other ways)
 
 ```    
 
@@ -558,8 +562,7 @@ Once logged in, as the 'ubuntu' user, run the following commands:
 ### Run Remote Slurm Tests On Headnode
 
 ```bash
-#!/bin/zsh
-source ./bin/daylily-run-ephemeral-cluster-remote-tests $pem_file $region $AWS_PROFILE
+./bin/daylily-run-ephemeral-cluster-remote-tests $pem_file $region $AWS_PROFILE
 ```
 
 A successful test will look like this:
@@ -579,7 +582,6 @@ pcluster list-clusters --region $REGION
 [See the instructions here](#first-time-logging-into-head-node) to confirm the headnode is configured and ready to run the daylily pipeline.
 
 
-
 <p valign="middle"><img src="docs/images/000000.png" valign="bottom" ></p>
 
 # Costs
@@ -777,7 +779,7 @@ ssh -i $pem_file ubuntu@$cluster_ip_address
 ##### Facilitated
 
 ```bash
-AWS_PROFILE=<profile_name>
+export AWS_PROFILE=<profile_name>
 bin/daylily-ssh-into-headnode 
 ```
 
@@ -813,7 +815,7 @@ From your remote terminal that you created the cluster with, run the following c
 ```bash
 conda activate DAYCLI
 
-source ./bin/daylily-cfg-headnode $PATH_TO_PEM $CLUSTER_AWS_REGION $AWS_PROFILE
+./bin/daylily-cfg-headnode $PATH_TO_PEM $CLUSTER_AWS_REGION $AWS_PROFILE
 ```
 
 > If the problem persists, ssh into the headnode, and attempt to run the commands as the ubuntu user which are being attempted by the `daylily-cfg-headnode` script.
diff --git a/bin/calc_daylily_aws_cost_estimates.py b/bin/calc_daylily_aws_cost_estimates.py
index dc421eaf..95b8fb14 100755
--- a/bin/calc_daylily_aws_cost_estimates.py
+++ b/bin/calc_daylily_aws_cost_estimates.py
@@ -1,3 +1,5 @@
+#!/bin/env python
+
 from daylib.day_cost_ec2 import AWSGenomicsAnalyzer
 
 def main():
diff --git a/bin/calcuate_spotprice_for_cluster_yaml.py b/bin/calcuate_spotprice_for_cluster_yaml.py
index e2b90858..2ee53b66 100755
--- a/bin/calcuate_spotprice_for_cluster_yaml.py
+++ b/bin/calcuate_spotprice_for_cluster_yaml.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+
 import subprocess
 import statistics
 import argparse
diff --git a/bin/cat_input_files.sh b/bin/cat_input_files.sh
index 322f1933..72c287ef 100755
--- a/bin/cat_input_files.sh
+++ b/bin/cat_input_files.sh
@@ -1,10 +1,5 @@
 #!/bin/bash
 
-# Ensure compatibility with zsh and bash
-if [ -n "$ZSH_VERSION" ]; then
-  emulate -LR bash  # Ensure bash-like behavior in zsh
-fi
-
 # Display usage information
 usage() {
   echo "Usage: $0 -s SAMPLENAME -p SAMPLE_MATCH_PATTERN -i INPUT_DIR -o OUTPUT_DIR"
@@ -42,7 +37,7 @@ if [[ ! -d "$OUTPUT_DIR" ]]; then
 fi
 
 echo ""
-echo ">>>  >> > THIS IS A SIMPLE UTILITY AND NOT PRODUCTION TESTED FOR YOUR USE CASE < <<  <<<"
+echo ">>>  >> > THIS IS A SIMPLE UTILITY AND NOT PRODUCTION TESTED < <<  <<<"
 echo ""
 sleep 2
 
diff --git a/bin/check_aws_permissions.sh b/bin/check_aws_permissions.sh
old mode 100644
new mode 100755
diff --git a/bin/check_current_spot_market_by_zones.py b/bin/check_current_spot_market_by_zones.py
index cb717cdc..e773ef28 100755
--- a/bin/check_current_spot_market_by_zones.py
+++ b/bin/check_current_spot_market_by_zones.py
@@ -466,6 +466,17 @@ def main():
     if args.profile == "SETME":
         print(f"\n\nERROR:: Your AWS_PROFILE is set to >{os.getenv('AWS_PROFILE')}<, Please set your AWS_PROFILE environment variable and specify the same string with --profile.\n")
         raise SystemExit
+    if os.environ.get('AWS_PROFILE','') == '':
+        os.environ['AWS_PROFILE'] = args.profile
+    elif args.profile != os.environ['AWS_PROFILE']:
+        print(f"\n\nERROR:: Your AWS_PROFILE is set to >{os.getenv('AWS_PROFILE')}<, Please set your AWS_PROFILE environment variable and specify the same string with --profile.\n")
+        raise SystemExit
+    elif args.profile == os.environ['AWS_PROFILE']:
+        print(f"\n\nAWS_PROFILE is set to >{os.getenv('AWS_PROFILE')}< and profile passed is >{args.profile}<, all good.\n")
+    else:
+        print(f"\n\nAWS_PROFILE is set to >{os.getenv('AWS_PROFILE')}< and profile passed is >{args.profile}<, there is a problem.\n")
+        raise SystemExit
+
     
     zones = args.zones.split(',')
     spot_data = collect_spot_prices(instance_types, zones, args.profile)
diff --git a/bin/check_system_pkgs.sh b/bin/check_prereq_sw.sh
similarity index 83%
rename from bin/check_system_pkgs.sh
rename to bin/check_prereq_sw.sh
index 4e9ce48f..17791e79 100755
--- a/bin/check_system_pkgs.sh
+++ b/bin/check_prereq_sw.sh
@@ -2,9 +2,8 @@
 
 # Set required versions
 required_versions=(
-    "python3:3.12.8"
+    "python3:3.11.0"
     "git:2.46.0"
-    "jq:1.7.1"
     "wget:1.25.0"
     "aws:2.22.4"
 )
@@ -14,9 +13,8 @@ pass_on_warn=${pass_on_warn:-0}
 
 # Function to compare versions
 check_version() {
-    local tool=$1
-    local required=$2
-    local current=$3
+    local required=$1
+    local current=$2
 
     if [[ "$(printf '%s\n' "$required" "$current" | sort -V | head -n1)" != "$required" ]]; then
         return 1 # Current version is less than required
@@ -38,12 +36,13 @@ check_tool() {
     fi
 
     # Check version
-    if ! check_version "$tool" "$required_version" "$current_version"; then
+    if ! check_version "$required_version" "$current_version"; then
         echo "Error: $tool version $current_version does not meet the required version $required_version."
         [[ "$pass_on_warn" -eq 1 ]] && return 0 || exit 1
     fi
 
-    echo "$tool version $current_version meets the requirement of $required_version or higher."
+    # Print success message if version is sufficient
+    echo "$tool version $current_version meets the required version $required_version or higher."
 }
 
 # Loop through required tools and check
@@ -58,9 +57,6 @@ for entry in "${required_versions[@]}"; do
         git)
             check_tool "git" "$required_version" "git --version | awk '{print \$3}'"
             ;;
-        jq)
-            check_tool "jq" "$required_version" "jq --version | sed 's/jq-//g'"
-            ;;
         wget)
             check_tool "wget" "$required_version" "wget --version | head -n1 | awk '{print \$3}'"
             ;;
diff --git a/bin/create_budget.sh b/bin/create_budget.sh
index c1c231b7..a69827de 100755
--- a/bin/create_budget.sh
+++ b/bin/create_budget.sh
@@ -78,9 +78,9 @@ write_or_append_tags_to_s3() {
 
   echo "Writing or appending tags to S3 file: $S3_BUCKET_PATH" url: $S3_BUCKET_URL
   # Check if the file exists in S3
-  if aws s3 ls "$S3_BUCKET_PATH" > /dev/null 2>&1; then
+  if aws s3 ls "$S3_BUCKET_PATH" --profile $AWS_PROFILE > /dev/null 2>&1; then
     echo "File exists. Downloading the existing file."
-    aws s3 cp "$S3_BUCKET_PATH" "$TEMP_LOCAL_FILE" --region "$REGION"
+    aws s3 cp "$S3_BUCKET_PATH" "$TEMP_LOCAL_FILE" --region "$REGION" --profile $AWS_PROFILE
 
     if [[ $? -ne 0 ]]; then
       echo "ERROR: Failed to download existing file from S3."
@@ -97,7 +97,7 @@ write_or_append_tags_to_s3() {
 
   # Upload the updated file back to S3
   echo "Uploading updated file to S3..."
-  aws s3 cp "$TEMP_LOCAL_FILE" "$S3_BUCKET_PATH" --region "$REGION"
+  aws s3 cp "$TEMP_LOCAL_FILE" "$S3_BUCKET_PATH" --region "$REGION" --profile $AWS_PROFILE
 
   if [[ $? -eq 0 ]]; then
     echo "Successfully updated S3 file: $S3_BUCKET_PATH"
@@ -153,12 +153,12 @@ BUDGET_JSON=$(echo "$BUDGET_TEMPLATE" | \
 TEMP_BUDGET_JSON=$(mktemp)
 echo "$BUDGET_JSON" > "$TEMP_BUDGET_JSON"
 
-ACCOUNT_ID=$(aws sts get-caller-identity --query Account --output text)
+ACCOUNT_ID=$(aws sts get-caller-identity --query Account --output text --profile $AWS_PROFILE)
 
 # Create the budget using AWS CLI
 echo "Creating budget for project: $PROJECT_NAME with amount: $AMOUNT USD in region: $REGION"
 aws budgets create-budget --account-id "$ACCOUNT_ID" \
-    --budget file://"$TEMP_BUDGET_JSON" --region "$REGION"
+    --budget file://"$TEMP_BUDGET_JSON" --region "$REGION" --profile $AWS_PROFILE
 
 # Check if the budget creation succeeded
 if [[ $? -eq 0 ]]; then
@@ -169,7 +169,7 @@ if [[ $? -eq 0 ]]; then
   IFS=',' read -ra THRESHOLD_ARRAY <<< "$THRESHOLDS"
   for threshold in "${THRESHOLD_ARRAY[@]}"; do
     echo P:$PROJECT_NAME T:$threshold E:$EMAIL R:$REGION A:$AMOUNT AI:$ACCOUNT_ID 
-    aws budgets create-notification --account-id "$ACCOUNT_ID" \
+    aws budgets create-notification --account-id "$ACCOUNT_ID" --profile $AWS_PROFILE \
       --budget-name "$PROJECT_NAME" \
       --notification '{"ComparisonOperator":"GREATER_THAN","NotificationType":"ACTUAL","Threshold":'"$threshold"',"ThresholdType":"PERCENTAGE"}' \
       --region "$REGION"   --subscribers '[{"Address":"'"$EMAIL"'","SubscriptionType":"EMAIL"}]' 
diff --git a/bin/daylily-analysis-samples-to-manifest b/bin/daylily-analysis-samples-to-manifest
deleted file mode 100755
index 63d4a088..00000000
--- a/bin/daylily-analysis-samples-to-manifest
+++ /dev/null
@@ -1,202 +0,0 @@
-#!/usr/bin/env bash
-
-# Neon color scheme
-INFO="\033[1;36m"
-WARN="\033[1;33m"
-ERROR="\033[1;31m"
-SUCCESS="\033[1;32m"
-RESET="\033[0m"
-
-info() { echo -e "${INFO}[INFO]${RESET} $1"; }
-warn() { echo -e "${WARN}[WARN]${RESET} $1"; }
-error() { echo -e "${ERROR}[ERROR]${RESET} $1"; exit 1; }
-success() { echo -e "${SUCCESS}[SUCCESS] $1"; }
-
-AM_OUT_FILE="na"
-
-check_dependencies() {
-  for cmd in ssh; do
-    if ! command -v $cmd &>/dev/null; then
-      error "Required command '$cmd' is not installed."
-    fi
-  done
-}
-
-validate_args() {
-  if [[ "$1" != "local" && "$1" != "remote" ]]; then
-    error "First argument must be 'local' or 'remote'."
-  fi
-  if [[ ! -f "$2" ]]; then
-    error "Sample sheet '$2' does not exist."
-  fi
-}
-
-determine_sex() {
-  local n_x=$1
-  local n_y=$2
-  if [[ "$n_x" -eq 2 && "$n_y" -eq 0 ]]; then
-    echo "female"
-  elif [[ "$n_x" -eq 1 && "$n_y" -eq 1 ]]; then
-    echo "male"
-  else
-    echo "na"
-  fi
-}
-
-validate_stage_target() {
-  local stage_target="$1"
-  local mode="$2"
-  local cluster_ip="$3"
-  local pem_file="$4"
-  local cluster_user="$5"
-
-  info "Validating STAGE_TARGET: $mode  $stage_target "
-  if [[ ! "$stage_target" =~ ^/fsx ]]; then
-    error "STAGE_TARGET '$stage_target' must begin with '/fsx'."
-  fi
-
-  if [[ "$mode" == "remote" ]]; then
-    info "Validating STAGE_TARGET on remote cluster: $stage_target"
-    ssh -i "$pem_file" "$cluster_user@$cluster_ip" "if [[ ! -d \"$stage_target\" ]]; then mkdir -p  \"$stage_target\"; fi" \
-      || error "Failed to create STAGE_TARGET directory on remote: $stage_target"
-  else
-    if [[ ! -d "$stage_target" ]]; then
-      info "Creating STAGE_TARGET directory locally: $stage_target"
-      mkdir -p "$stage_target" || error "Failed to create STAGE_TARGET directory: $stage_target"
-    fi
-  fi
-}
-
-stage_data_files() {
-  local r1_src="$1"
-  local r2_src="$2"
-  local stage_target="$3"
-  local sample_prefix="$4"
-  local mode="$5"
-  local cluster_ip="$6"
-  local pem_file="$7"
-  local cluster_user="$8"
-
-  local r1_dest="${stage_target}/${sample_prefix}.R1.fastq.gz"
-  local r2_dest="${stage_target}/${sample_prefix}.R2.fastq.gz"
-
-  if [[ "$mode" == "remote" ]]; then
-    info "Staging R1 to remote: $r1_dest"
-
-    ssh -i "$pem_file" "$cluster_user@$cluster_ip"  "if [[ -f '$r1_dest' ]]; then exit 1; fi" && \
-    echo "File does not exist on remote" || \
-    { echo "Error: File '$r1_dest' already exists on remote."; exit 1; }
-
-    scp -i "$pem_file" "$r1_src" "${cluster_user}@${cluster_ip}:${r1_dest}" || error "Failed to stage R1 to remote."
-    success "R1 staged to remote: $r1_dest"
-
-    ssh -i "$pem_file" "$cluster_user@$cluster_ip"  "if [[ -f '$r2_dest' ]]; then exit 1; fi" && \
-    echo "File does not exist on remote" || \
-    { echo "Error: File '$r2_dest' already exists on remote."; exit 1; }
-    info "Staging R2 to remote: $r2_dest"
-    scp -i "$pem_file" "$r2_src" "${cluster_user}@${cluster_ip}:${r2_dest}" || error "Failed to stage R2 to remote."
-    success "R2 staged to remote: $r2_dest"
-  else
-    [[ ! -e "$r1_src" ]] && error "R1 file '$r1_src' does not exist."
-    [[ ! -e "$r2_src" ]] && error "R2 file '$r2_src' does not exist."
-
-    cp "$r1_src" "$r1_dest" || error "Failed to copy R1: $r1_src to $r1_dest"
-    success "R1 staged locally: $r1_dest"
-
-    cp "$r2_src" "$r2_dest" || error "Failed to copy R2: $r2_src to $r2_dest"
-    success "R2 staged locally: $r2_dest"
-  fi
-}
-
-parse_and_validate_tsv() {
-  local input_file="$1"
-  local mode="$2"
-  local cluster_ip="$3"
-  local pem_file="$4"
-  local cluster_user="$5"
-
-
-  while IFS=$'\t' read -r RUN_ID SAMPLE_ID SAMPLE_TYPE LIB_PREP SEQ_PLATFORM LANE SEQBC_ID PATH_TO_CONCORDANCE_DATA_DIR R1_FQ R2_FQ STAGE_DIRECTIVE STAGE_TARGET SUBSAMPLE_PCT IS_POS_CTRL IS_NEG_CTRL N_X N_Y; do
-    [[ "$LANE" != "0" ]] && error "Invalid LANE value '$LANE'. Only '0' is allowed."
-    [[ "$IS_POS_CTRL" != "na" || "$IS_NEG_CTRL" != "na" ]] && error "Positive or Negative Control columns are not enabled yet."
-
-    echo "Processing: $RUN_ID $SAMPLE_ID $SAMPLE_TYPE $LIB_PREP $SEQ_PLATFORM $LANE $SEQBC_ID $PATH_TO_CONCORDANCE_DATA_DIR $R1_FQ $R2_FQ $STAGE_DIRECTIVE $STAGE_TARGET $SUBSAMPLE_PCT $IS_POS_CTRL $IS_NEG_CTRL $N_X $N_Y"
-
-    AS_IN_FILE="${STAGE_TARGET}/${RUN_ID}.analysis_samples.tsv"
-    tmp_am_out_file="./${RUN_ID}.analysis_manifest.csv.tmp"
-    touch "$tmp_am_out_file"
-    AM_OUT_FILE="${STAGE_TARGET}/${RUN_ID}.analysis_manifest.csv"
-  done < <(tail -n +2 "$input_file")
-
-  echo "ASIO $AS_IN_FILE ... $AM_OUT_FILE ... $tmp_am_out_file"
-
-  echo "samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct" >"$tmp_am_out_file"
-
-  while IFS=$'\t' read -r RUN_ID SAMPLE_ID SAMPLE_TYPE LIB_PREP SEQ_PLATFORM LANE SEQBC_ID PATH_TO_CONCORDANCE_DATA_DIR R1_FQ R2_FQ STAGE_DIRECTIVE STAGE_TARGET SUBSAMPLE_PCT IS_POS_CTRL IS_NEG_CTRL N_X N_Y; do
-    [[ "$LANE" != "0" ]] && error "Invalid LANE value '$LANE'. Only '0' is allowed."
-    [[ "$IS_POS_CTRL" != "na" || "$IS_NEG_CTRL" != "na" ]] && error "Positive or Negative Control columns are not enabled yet."
-
-    echo "Processing: $RUN_ID $SAMPLE_ID $SAMPLE_TYPE $LIB_PREP $SEQ_PLATFORM $LANE $SEQBC_ID $PATH_TO_CONCORDANCE_DATA_DIR $R1_FQ $R2_FQ $STAGE_DIRECTIVE $STAGE_TARGET $SUBSAMPLE_PCT $IS_POS_CTRL $IS_NEG_CTRL $N_X $N_Y"
-    local biological_sex=$(determine_sex "$N_X" "$N_Y")
-    local sample_prefix="${RUN_ID}_${SAMPLE_ID}_${SAMPLE_TYPE}_${LANE}-${SEQBC_ID}"
-
-    echo "----SD $STAGE_DIRECTIVE"
-    validate_stage_target "$STAGE_TARGET" "$mode" "$cluster_ip" "$pem_file" "$cluster_user"
-
-    if [[ "$STAGE_DIRECTIVE" == "stage_data" ]]; then
-      stage_data_files "$R1_FQ" "$R2_FQ" "$STAGE_TARGET" "$sample_prefix" "$mode" "$cluster_ip" "$pem_file" "$cluster_user"
-    fi
-
-    local staged_r1="${STAGE_TARGET}/${sample_prefix}.R1.fastq.gz"
-    local staged_r2="${STAGE_TARGET}/${sample_prefix}.R2.fastq.gz"
-    echo "${sample_prefix},${sample_prefix},${sample_prefix},${SAMPLE_TYPE},${RUN_ID},${SAMPLE_ID},${LANE}-${SEQBC_ID},${staged_r1},${staged_r2},${biological_sex},na,${PATH_TO_CONCORDANCE_DATA_DIR},na,na,${SAMPLE_TYPE},merge,${SAMPLE_ID},${SEQ_PLATFORM},${LIB_PREP},19,${SUBSAMPLE_PCT}" >>"$tmp_am_out_file"
-  done < <(tail -n +2 "$input_file")
-
-
-  if [[ "$mode" == "remote" ]]; then
-
-    ssh -i "$pem_file" "$cluster_user@$cluster_ip"  "if [[ -f '$AS_IN_FILE' ]]; then exit 1; fi" && \
-    echo "File does not exist on remote" || \
-      { echo "Error: File '$AS_IN_FILE' already exists on remote."; exit 1; }
-
-    scp -i "$pem_file" "$input_file" "${cluster_user}@${cluster_ip}:${AS_IN_FILE}" || error "Failed to stage R1 to remote."
-    success "Analysis samples $input_file moved to remote: scp -i $pem_file $input_file ${cluster_user}@${cluster_ip}:$AS_IN_FILE"
-
-
-    ssh -i "$pem_file" "$cluster_user@$cluster_ip"  "if [[ -f '$AM_OUT_FILE' ]]; then exit 1; fi" && \
-    echo "File does not exist on remote" || \
-      { echo "Error: File '$AM_OUT_FILE' already exists on remote."; exit 1; }
-
-    scp -i "$pem_file" "$tmp_am_out_file" "${cluster_user}@${cluster_ip}:${AM_OUT_FILE}" || error "Failed to stage R1 to remote."
-    success "$tmp_am_out_file  moved to remote: scp -i $pem_file $input_file ${cluster_user}@${cluster_ip}:$AM_OUT_FILE"
-
-
-
-  else
-    echo "pass on copy $AS_IN_FILE"
-  fi
-}
-
-main() {
-  local mode="$1"
-  local input_file="$2"
-  local cluster_ip="$3"
-  local pem_file="$4"
-  local cluster_user="$5"
-
-  check_dependencies
-  validate_args "$@"
-
-  #if [[ "$mode" == "remote" ]]; then
-  #  ssh -i "$pem_file" "$cluster_user@$cluster_ip" \
-  #    "if [[ ! -d '/fsx/staged_sample_data' ]]; then mkdir '/fsx/staged_sample_data'; fi" \
-  #    || error "Failed to create '/fsx/staged_sample_data' directory on remote cluster."
-  #else
-  #  mkdir  "/fsx/staged_sample_data" || error "Failed to create local '/fsx/staged_sample_data'."
-  #fi
-
-  parse_and_validate_tsv "$input_file" "$mode" "$cluster_ip" "$pem_file" "$cluster_user"
-  success "Manifest generated: $AM_OUT_FILE"
-}
-
-main "$@"
diff --git a/bin/daylily-cfg-headnode b/bin/daylily-cfg-headnode
old mode 100644
new mode 100755
index 278eddb5..841cdfc6
--- a/bin/daylily-cfg-headnode
+++ b/bin/daylily-cfg-headnode
@@ -1,13 +1,7 @@
-#!/bin/zsh
+#!/bin/bash
 
 # Daylily Headnode Configuration Script
 
-# Ensure the script is sourced, not executed directly
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    echo "This script should be sourced, not executed directly. Please use 'source THISSCRIPT' to run."
-    exit 1
-fi
-
 # Capture arguments for PEM file and region
 pem_file=$1
 region=$2
@@ -142,7 +136,7 @@ echo " "
 echo "___bonus round___"
 echo "Would you like to start building various caches needed to run jobs? [y/n]"
 
-timeout 120 bash -c 'read -p "Press y to start or n to skip: " REPLY && echo "$REPLY"' && export REPLY=$REPLY
+timeout 30 bash -c 'read -p "Press y to start or n to skip: " REPLY && echo "$REPLY"' && export REPLY=$REPLY
 
 if [[ "$REPLY" == "y" ]]; then
     # start building the minimal cached envs
@@ -161,6 +155,6 @@ echo "And, you may now access the headnode via the PCUI, via 'source bin/daylily
 echo -e "       ssh -i $pem_file ubuntu@$cluster_ip_address\n"
 echo " "
 echo "If you wish to run some remote tests, you can do so with the following command:"
-echo -e "      . bin/daylily-run-ephemeral-cluster-remote-tests $pem_file $region $aws_profile\n"
+echo -e "   ./bin/daylily-run-ephemeral-cluster-remote-tests $pem_file $region $aws_profile\n"
 echo " "
 echo "...fin"
diff --git a/bin/daylily-create-ephemeral-cluster b/bin/daylily-create-ephemeral-cluster
old mode 100644
new mode 100755
index c57e4983..2e39d1b2
--- a/bin/daylily-create-ephemeral-cluster
+++ b/bin/daylily-create-ephemeral-cluster
@@ -1,38 +1,15 @@
-#!/bin/zsh
+#!/bin/bash
 
 
-# Function to check if the script is sourced
-is_sourced() {
-    # If the script is sourced, BASH_SOURCE[0] != $0
-    [[ "${BASH_SOURCE[0]}" != "${0}" ]]
-}
-
-CURR_SHELL=$(ps -p $$ -o comm=)
-echo $CURR_SHELL
-
-if [[ "$CURR_SHELL" != "zsh" ]]; then
-    echo "ERROR: This script must be executed from a zsh shell. please run 'zsh' and re-run this."
-    ~/miniconda3/bin/conda init zsh || echo "conda init failed, possibly legit if conda is not installed yet."
-
-    if is_sourced; then
-        # If sourced, use 'return' to avoid exiting the shell
-        return 3
-    else
-        # If executed, use 'exit' to terminate the script
-        exit 3
-    fi
-fi
-
-echo "Now running in zsh. Continuing script execution..."
-# Your script logic here
-emulate -L bash
+CURR_SHELL=$(. bin/retshell)
+echo "$CURR_SHELL"
 
 # Default configuration
-pass_on_warn=''  # Default for warnings causing failures
+pass_on_warn=0  # Default for warnings causing failures
 
 # Function to display help
 usage() {
-    echo "Usage: source $0 [--region-az REGION-AZ] [--pass-on-warn]"
+    echo "Usage: $0 --profile AWS_PROFILE [--region-az REGION-AZ] [--pass-on-warn]"
     echo "       --region-az REGION-AZ   Specify the AWS region and availability zone (tested w us-west-2c/d)"
     echo "       --pass-on-warn          Allow warnings to pass without failure (default: false)"
     echo "       --profile  aws profile to use"
@@ -42,12 +19,12 @@ usage() {
 # Check if script is sourced with no arguments
 if [[ $# -eq 0 ]]; then
     usage
-    return 0
+    exit 0
 fi
 
 if [ -z "$AWS_PROFILE" ]; then
     echo "Error: AWS_PROFILE is not set."
-    return 1  # Exit the function with an error status
+    exit 1  # Exit the function with an error status
 fi
 
 # Parse command-line arguments
@@ -55,16 +32,16 @@ while [[ $# -gt 0 ]]; do
     case "$1" in
         --region-az)
             region_az="$2"
-            region="${region_az::-1}"  # Remove the last character from the AZ
+            region="${region_az:0:${#region_az}-1}"
             shift 2
             ;;
         --pass-on-warn)
-            pass_on_warn=true
+            pass_on_warn="1"
             shift
             ;;
         -h|--help)
             usage
-            return 0  # Use exit instead of return
+            exit 0
             ;;
         --profile)
             AWS_PROFILEIN="$2"
@@ -73,31 +50,24 @@ while [[ $# -gt 0 ]]; do
         *)
             echo "Error: Unknown option: $1"
             usage
-            return 3  # Use exit instead of return
+            exit 3
             ;;
     esac
 done
 
-
-# Ensure the script is sourced
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    echo "Error: This script must be sourced, not executed directly. Use 'source $0' to run."
-    exit 3
-fi
-
 if [[ -z "$AWS_PROFILE" ]]; then
     echo "Error: --profile flag not set"
-    return 3  # Exit the function with an error status
+    exit 3  # Exit the function with an error status
 fi
 
 if [[ "$AWS_PROFILE" != "$AWS_PROFILEIN" ]]; then
     echo "Error: AWS_PROFILE and --profile must match: $AWS_PROFILE and $AWS_PROFILEIN"
-    return 3  # Exit the function with an error status
+    exit 3  # Exit the function with an error status
 fi
 
 if [[ -z "$region_az" ]]; then
     echo "Error: --region-az flag not set"
-    return 3  # Exit the function with an error status
+    exit 3  # Exit the function with an error status
 fi
 
 # Extract the last character
@@ -108,12 +78,12 @@ if [[ "$az_char" =~ [a-zA-Z] ]]; then
     echo "The last character of --region-az ${region_az} '$az_char' is a letter."
 else
     echo "ERROR: The last character of --region-az ${region_az} '$az_char' is a NOT letter."
-    return 3  # Exit the function with an error status
+    exit 3  # Exit the function with an error status
 fi
 
 if [[ "$AWS_PROFILEIN" != "$AWS_PROFILE" ]]; then
     echo "Error: AWS_PROFILE and --profile must match: $AWS_PROFILE and $AWS_PROFILEIN"
-    return 3  # Exit the function with an error status
+    exit 3  # Exit the function with an error status
 fi
 
 AWS_PROFILE=$AWS_PROFILE
@@ -123,58 +93,71 @@ echo "YOUR AWS_PROFILE IS NOW SET TO: $AWS_PROFILE"
 handle_warning() {
     local message="$1"
     echo -e "WARNING: $message"
-    echo "If appropriate, consider setting --pass-on-warn to continue without failure. -$pass_on_warn-"
-    if [[ "$pass_on_warn" == "" ]]; then
-        echo "exiting"
-        return 3
+    echo "If appropriate, consider setting --pass-on-warn to continue without failure. Current setting: $pass_on_warn"
+    if [[ "$pass_on_warn" != "1" ]]; then
+        echo "Exiting due to warning."
+        exit 3
     fi
 }
 
 validate_region() {
   echo "REGION:" $1 
 }
+echo "DEBUG: pass_on_warn after parsing: $pass_on_warn"
 
-echo "Welcome to the Daylily CLI Setup"
-echo "Daylily is tested to run in region $region (AZ: $region_az)."
-echo "Please ensure your ~/.aws/config file matches this region."
-
-### Conda Environment Setup
-
-
-# Ensure Conda exists
-conda --version &> /dev/null
-if [[ $? -ne 0 ]]; then
-    echo "Error: Conda is not available in this shell. Attempting to determine if autoinstall is possible."
-    
-    source bin/install_miniconda
+# Check if system packages are installed
+./bin/check_prereq_sw.sh
+if [ $? -ne 0 ]; then
+    handle_warning "There were problems detected with pre-requisites, and the warnings bypassed. Run './bin/check_prereq_sw.sh' for more information ." 
+    if [[ $? -ne 0 ]]; then
+        echo "Error: System package check failed, investigate or run again with or use --pass-on-warn."
+        exit 3
+    fi
 fi
 
+# Ensure Conda exists
 conda --version &> /dev/null
 if [[ $? -ne 0 ]]; then
-    echo "Error: Conda is not available in this shell despite attempting an autoinstall. Exiting."
-    return 3
+    echo ">  > Error <  <"
+    echo "Conda is not available in this shell (version >= 24.0.0)."
+    echo "Please run the following command to install miniconda. *warning*, if you are using homebrew conda, things might get wobbly."
+    echo ""
+    echo "To install miniconda, run:"
+    echo "    ./bin/install_miniconda # and once installed, open a new shell and run "
+    exit 1
 fi
 
+# Check conda version is sufficent
 # Required version
-required_version="24.11.1"
-
-# Check if conda is installed
-if ! command -v conda &> /dev/null; then
-    echo "Error: conda is not installed."
-    return 3
-fi
+required_version="24.0.0"
 
 # Get the current conda version
 current_version=$(conda --version | awk '{print $2}')
 
 # Compare versions
 if [[ "$(printf '%s\n' "$required_version" "$current_version" | sort -V | head -n1)" != "$required_version" ]]; then
-    echo "Error: Conda version $current_version is less than the required version $required_version."
-    return 3
+    echo "Error: Conda version $current_version is less than the required version $required_version ."
+    exit 3
 fi
 
 echo "Conda version $current_version meets the requirement of $required_version or higher."
 
+
+# Check if the Conda environment DAYCLI is active
+if [[ "$CONDA_DEFAULT_ENV" == "DAYCLI" ]]; then
+    echo "The Conda environment DAYCLI is active, proceeding."
+else
+    echo "The Conda environment DAYCLI is not active or missing."
+    echo ""
+    echo "Please activate the DAYCLI environment by running:"
+    echo "    conda activate DAYCLI"
+    echo ""
+    echo "If the environment does not exist, create it by running:"
+    echo "    ./bin/init_daycli"
+    exit 3
+fi
+
+
 # Activate or create the Daylily CLI conda environment
 if conda env list | grep -q "^DAYCLI "; then
     echo "Conda environment 'DAYCLI' already exists. Activating it."
@@ -183,7 +166,7 @@ else
     source bin/init_daycli
     if [[ $? -ne 0 ]]; then
         echo "Error: Failed to create the 'DAYCLI' environment. Exiting."
-        return 3
+        exit 3
     fi
 fi
 conda activate DAYCLI
@@ -198,7 +181,7 @@ if [[ "$pcluster_version" != "$expected_pcluster_version" ]]; then
     handle_warning "Warning: Expected pcluster version $expected_pcluster_version, but found version $pcluster_version."
     if [[ $? -ne 0 ]]; then
         echo "Error: pcluster version mis-match:  expected:$expected_pcluster_version , detected:$pcluster_version ."
-        return 3
+        exit 3
     fi
 fi
 
@@ -207,13 +190,13 @@ fi
 echo "Verifying AWS credentials..."
 if ! aws sts get-caller-identity --region "$region" --profile $AWS_PROFILE  &> /dev/null; then
     echo "Error: AWS credentials are invalid or do not have access to the AWS account in region $region."
-    return 3
+    exit 3
 else
     echo "AWS credentials verified successfully."
 fi
 
 # Call the region validation function
-validate_region "$region" || return 3
+validate_region "$region" || exit 3
 
 AWS_ACCOUNT_ID=$(aws sts get-caller-identity --query Account --output text  --profile $AWS_PROFILE )
 
@@ -242,10 +225,10 @@ else
         echo "Proceeding anyway..."
     elif [ "$CHOICE" -eq 2 ]; then
         echo "Exiting."
-        return 3 2>/dev/null || exit 3
+        exit 3 2>/dev/null || exit 3
     else
         echo "Invalid choice. Exiting."
-        return 3 2>/dev/null || exit 3
+        exit 3 2>/dev/null || exit 3
     fi
 fi
 
@@ -263,7 +246,7 @@ check_quota() {
 
     if [[ $? -ne 0 ]]; then
         handle_warning "Error: Unable to retrieve quota for $resource_name."
-        return 3
+        exit 3
     fi
 
     quota_value=$(echo "$quota" | jq -r '.Quota.Value')
@@ -272,7 +255,7 @@ check_quota() {
         handle_warning "Warning: $resource_name quota is below the recommended $recommended_count. Current quota: $quota_value."
         if [[ $? -ne 0 ]]; then
             echo "quota check failed"
-            return 3
+            exit 3
         fi
     else
         echo "$resource_name quota is sufficient: $quota_value."
@@ -286,42 +269,42 @@ echo "Performing AWS quota checks..."
 # Dedicated Instances
 check_quota "Spot vCPU Max" "L-1216C47A" 20 ec2
 if [[ $? -ne 0 ]]; then
-    return 3
+    exit 3
 fi
 echo ""
 
 # Spot vCPU Max Quota 
 check_quota "Spot vCPU Max" "L-34B43A08" 208 ec2
 if [[ $? -ne 0 ]]; then
-    return 3
+    exit 3
 fi
 echo ""
 
 # VPC Quota (Default: 5 per region)
 check_quota "VPCs" "L-F678F1CE" 4 vpc
 if [[ $? -ne 0 ]]; then
-    return 3
+    exit 3
 fi
 echo ""
 
 # Elastic IP Quota (Default: 5 per region)
 check_quota "Elastic IPs" "L-0263D0A3" 4 ec2
 if [[ $? -ne 0 ]]; then
-    return 3
+    exit 3
 fi
 echo ""
 
 # NAT Gateway Quota (Default: 5 per AZ)
 check_quota "NAT Gateways" "L-FE5A380F" 4 vpc
 if [[ $? -ne 0 ]]; then
-    return 3
+    exit 3
 fi
 echo ""
 
 # Internet Gateway Quota (Default: 5 per region)
 check_quota "Internet Gateways" "L-A4707A72" 4 vpc
 if [[ $? -ne 0 ]]; then
-    return 3
+    exit 3
 fi
 echo ""
 
@@ -389,7 +372,7 @@ echo ""
 if [[ ${#valid_keys[@]} -eq 0 ]]; then
     echo "No valid ED25519 keys with matching PEM files were found."
     echo "Please ensure the required keys are available in the $HOME/.ssh directory AND that the keypair name includes 'omics' in the name."
-    return 3
+    exit 3
 fi
 # Present valid keys to the user using 'select'
 echo "Select a valid ED25519 key with a matching PEM file:"
@@ -459,7 +442,7 @@ done <<< "$buckets"
 
 if [[ ${#matching_buckets[@]} -eq 0 ]]; then
     echo "No matching buckets found in region $region."
-    return 3
+    exit 3
 fi
 
 echo "Select a matching S3 bucket:"
@@ -481,13 +464,13 @@ check_s3_folder() {
         echo "Folder s3://$bucket/$folder/ exists."
     else
         echo "ERROR: Folder s3://$bucket/$folder/ does not exist."
-        return 1
+        exit 1
     fi
 }
 
 echo "Validating required folders in bucket: $selected_bucket"
-check_s3_folder "$bucket" "data" || return 3
-check_s3_folder "$bucket" "cluster_boot_config" || return 3 
+check_s3_folder "$bucket" "data" || exit 3
+check_s3_folder "$bucket" "cluster_boot_config" || exit 3 
 
 
 bucket_url="s3://$selected_bucket"
@@ -520,7 +503,7 @@ if [[ -z "$public_subnets" && -z "$private_subnets" ]]; then
     bin/init_cloudstackformation.sh ./config/day_cluster/pcluster_env.yml "$res_prefix" "$region_az" "$region" $AWS_PROFILE
 elif [[ -z "$public_subnets" || -z "$private_subnets"  ]]; then
     echo "Error: Incomplete setup. Ensure public and private subnets and the required ARN are available.  You might try running : bin/init_cloudstackformation.sh ./config/day_cluster/pcluster_env.yml $res_prefix $region_az $region $AWS_PROFILE"
-    return 1
+    exit 1
 else
     echo "All required resources are available."
 fi
@@ -577,7 +560,7 @@ echo ""
 # Function to validate cluster name
 validate_cluster_name() {
     if [[ ! "$1" =~ ^[a-zA-Z0-9\-]+$ ]] || [[ ${#1} -gt 25 ]]; then
-        return 1
+        exit 1
     else
         return 0
     fi
@@ -636,7 +619,7 @@ if [[ -z "$global_budget_exists" || "$global_budget_exists" == "None" ]]; then
 
     if [[ $? -ne 0 ]]; then
         echo "Error: Failed to create the budget. Exiting."
-        return 3
+        exit 3
     else
         echo "Budget '$global_budget_name' created successfully."
     fi
@@ -685,7 +668,7 @@ if [[ -z "$budget_exists" || "$budget_exists" == "None" ]]; then
 
     if [[ $? -ne 0 ]]; then
         echo "Error: Failed to create the budget. Exiting."
-        return 3
+        exit 3
     else
         echo "Budget '$budget_name' created successfully."
     fi
@@ -719,7 +702,7 @@ fi
 
 if [[ ! -f "$cluster_yaml" ]]; then
     echo "Error: YAML file '$cluster_yaml' does not exist."
-    return 3
+    exit 3
 fi 
 
 echo ""
@@ -852,7 +835,7 @@ if [[ $? -ne 0 ]]; then
     echo "Error: Failed to calculate spot bid prices."
     echo "This is likely due to a policy/permissions issue in AWS."
     echo "Please refer to the quickstart guide for more information on required policies."
-    return 3  # Use 'exit 3' if outside a function or script
+    exit 3  # Use 'exit 3' if outside a function or script
 fi
 echo ""
 
@@ -870,10 +853,10 @@ if [[ "$message" == "Request would have succeeded, but DryRun flag is set." ]];
     echo "Dry run successful. Proceeding with cluster creation."
 elif [[ "$DAY_BREAK" == "1" ]]; then
     echo "DAY_BREAK == '1'.  Exiting without creating the cluster."
-    return 0
+    exit 0
 else
     echo "Error: Dry run failed (  pcluster create-cluster -n $cluster_name -c $target_conf_fin --dryrun true --region $region   ). Exiting."
-    return 3
+    exit 3
 fi
 echo ""
 
diff --git a/bin/daylily-get-ephemperal-cluster-deets b/bin/daylily-get-ephemperal-cluster-deets
old mode 100644
new mode 100755
diff --git a/bin/daylily-run-ephemeral-cluster-remote-tests b/bin/daylily-run-ephemeral-cluster-remote-tests
old mode 100644
new mode 100755
index d9c57a2e..27c4e005
--- a/bin/daylily-run-ephemeral-cluster-remote-tests
+++ b/bin/daylily-run-ephemeral-cluster-remote-tests
@@ -1,13 +1,7 @@
-#!/bin/zsh
+#!/bin/bash
 
 # Daylily Headnode Configuration Script
 
-# Ensure the script is sourced, not executed directly
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    echo "This script should be sourced, not executed directly. Please use 'source THISSCRIPT' to run."
-    exit 1
-fi
-
 # Capture arguments for PEM file and region
 pem_file=$1
 region=$2
@@ -91,12 +85,12 @@ read REPLY
 if [[ "$REPLY" == "y" ]]; then
 
     ssh -i "$pem_file" ubuntu@"$cluster_ip_address"  -o StrictHostKeyChecking=no   -o UserKnownHostsFile=/dev/null \
-        "sudo su - $duser -c 'mkdir -p /fsx/analysis_results/ubuntu/daylily_remote_test && cd /fsx/analysis_results/ubuntu/daylily_remote_test &&  git clone https://github.com/Daylily-Informatics/daylily.git daylily_remote_test'"
+        "sudo su - $duser -c 'mkdir -p /fsx/analysis_results/ubuntu/daylily_remote_test && cd /fsx/analysis_results/ubuntu/daylily_remote_test &&  git clone https://github.com/Daylily-Informatics/daylily.git daylily'"
 
     session_name="cluster_test_$(date +%s)"  
     ssh -t -i "$pem_file" ubuntu@"$cluster_ip_address" -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null \
         "tmux new-session -d -s \"$session_name\" \
-        \"bash -c 'source ~/.bashrc && cd /fsx/analysis_results/ubuntu/daylily_remote_test && source dyinit && source bin/day_activate slurm hg38 remote && ./bin/day_run produce_snv_concordances -p -k -j 2 --config aligners=[\\\"strobe\\\",\\\"bwa2a\\\"] dedupers=[\\\"dppl\\\"] genome_build=\\\"hg38\\\" snv_callers=[\\\"deep\\\"]; bash'\"" && \
+        \"bash -c 'source ~/.bashrc && cd /fsx/analysis_results/ubuntu/daylily_remote_test/daylily && source dyinit && source bin/day_activate slurm hg38 remote && ./bin/day_run produce_snv_concordances -p -k -j 2 --config aligners=[\\\"strobe\\\",\\\"bwa2a\\\"] dedupers=[\\\"dppl\\\"] genome_build=\\\"hg38\\\" snv_callers=[\\\"deep\\\"]; bash'\"" && \
 
     echo "Tmux session >>> '$session_name' <<< started on the remote server."
     echo "You can monitor the session using the following command:"
diff --git a/bin/init_daycli b/bin/init_daycli
index 7fd96c5e..faa5db7a 100755
--- a/bin/init_daycli
+++ b/bin/init_daycli
@@ -1,77 +1,39 @@
 #!/bin/bash
 
-skip_warn=$1
-warn_msg=""
-
 mkdir -p ~/.config/daylily
 
-# Check if the script is running in Zsh and emulate Zsh behavior
-if [ -n "$ZSH_VERSION" ]; then
-    emulate -L zsh  # Ensure Zsh behaves like Zsh (if required)
-
-    # Check if the script is sourced or executed
-    if [ -n "$ZSH_EVAL_CONTEXT" ] && [[ "$ZSH_EVAL_CONTEXT" =~ :file$ ]]; then
-        echo "This script is sourced."
-    else
-        echo "Error: This script must be sourced, not executed directly. Use 'source $0' to run."
-        exit 3
-    fi
-fi
-
-# Ensure the script is sourced
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    echo "Error: This script must be sourced, not executed directly. Use 'source $0' to run."
-    exit 3
-fi
 
-# Check if system packages are installed
-bash bin/check_system_pkgs.sh
-if [ $? -ne 0 ]; then
-
-    if [ "$skip_warn" != "skip_warn" ]; then
-        warn_msg="There were problems detected with pre-requisites, and the warnings bypassed. Run 'bash bin/check_system_pkgs.sh' for more information." 
-    else
-        echo "Some system packages are missing or are the wrong version which may cause problems. Please review them by running: 'bash bin/check_system_pkgs.sh' for more information. You may proceed past this warning by passing the first argument as 'skip_warn'." 
-        return 1
-    fi
-fi
 
 # Ensure Conda exists
 if ! command -v conda &> /dev/null; then
-    echo "Error: Conda is not available in this shell. Attempting to install Miniconda..."
-    echo ""
+    echo "Error: Conda is not available in this shell. Please install Miniconda."
+    echo "Install with:"
 
-    echo "source ./bin/install_miniconda"
-    source ./bin/install_miniconda
+    echo "     ./bin/install_miniconda "
+    exit 3
 fi
 
-CURR_SHELL=$(ps -p $$ -o comm=)
-echo $CURR_SHELL
 if ! command -v conda &> /dev/null; then
-    echo "Error: Conda is not available in this shell. Autoinstall failed, please see the miniconda docs."
-    echo "*** If your shell (login:$SHELL , current:$CURR_SHELL) is bash, please check if conda init correctly updated both your .bashrc and .bash_profile with the conda initialization block. If present in one but not the other, copy it, open a new bash shell and try again (most commonly a problem with MACs). ***"   
-    return 1
+    echo "Error: Conda is not available in this shell. "
+    echo "Install with:"
+    echo "     ./bin/install_miniconda "
+    exit 1
 fi
 
 # Activate or create the Daylily CLI conda environment
 if conda env list | grep -q "^DAYCLI "; then
-    echo "Conda environment 'DAYCLI' already exists."
+    echo "Conda environment 'DAYCLI' already exists!"
+    echo "Activate with: "
+    echo "    conda activate DAYCLI"
+    exit 3
 else
     echo "Creating 'DAYCLI' environment."
     conda env create -y -n DAYCLI -f config/day/daycli.yaml
-    #conda create -y -n DAYCLI -c conda-forge python parallel jq nodejs==18.15.0 aws-parallelcluster==3.11.1 flask=2.2.5 pyyaml
-fi
-echo "Activating 'DAYCLI' environment."
-conda activate DAYCLI
-# Function to check if a Python package is installed
-check_and_install() {
-    PACKAGE=$1
-    VERSION=$2
-    if ! python -c "import $PACKAGE" &> /dev/null; then
-        echo "$PACKAGE not found. Installing $PACKAGE==$VERSION..."
-        pip install "$PACKAGE==$VERSION"
+    if [ $? -ne 0 ]; then
+        echo "Error: Failed to create 'DAYCLI' environment."
+        exit 1
     fi
-}
-
+fi
 
-echo "Daylily CLI environment is ready ($warn_msg)."
\ No newline at end of file
+echo "Daylily CLI environment is ready!  Activate with: "
+echo "    conda activate DAYCLI"
\ No newline at end of file
diff --git a/bin/install_miniconda b/bin/install_miniconda
old mode 100644
new mode 100755
index 33b033c3..60a043ad
--- a/bin/install_miniconda
+++ b/bin/install_miniconda
@@ -1,23 +1,5 @@
-# Ensure the script is sourced and not executed directly
-if [[ -n "$ZSH_VERSION" ]]; then
-    # Check if the script is being sourced in zsh
-    # Check if the script is sourced or executed
-    if [ -n "$ZSH_EVAL_CONTEXT" ] && [[ "$ZSH_EVAL_CONTEXT" =~ :file$ ]]; then
-        echo "This script is sourced, proceed"
-    else
-        echo "Error: This script must be sourced, not executed directly. Use 'source $0' to run."
-        exit 3
-    fi
-elif [[ -n "$BASH_VERSION" ]]; then
-    # Check if the script is being sourced in bash
-    if [[ "$0" == "${BASH_SOURCE[0]}" ]]; then
-        echo "This script must be sourced. Use: source $0 or . $0"
-        return 1
-    fi
-else
-    echo "Unsupported shell. Please use bash or zsh to run this script."
-    return 1
-fi
+
+
 
 # Check if Miniconda is already installed
 conda --version &> /dev/null
@@ -25,7 +7,7 @@ if [[ $? -ne 0 ]]; then
     echo "Miniconda is not installed. Proceeding with installation..."
 else
     echo "Miniconda is already installed. Please uninstall it before proceeding."
-    return 0
+    exit 0
 fi
 
 
@@ -49,7 +31,7 @@ if [[ -z "$MACHINE" ]]; then
             ;;
         *)
             echo "Unsupported architecture: $uname_output"
-            return 1
+            exit 1
             ;;
     esac
 fi
@@ -82,29 +64,68 @@ elif [[ "$MACHINE" == "linux_arm" ]]; then
 else
     echo "Unsupported machine type: $MACHINE"
     echo "Please visit https://docs.conda.io/en/latest/miniconda.html for manual installation instructions."
-    return 2
+    exit 2
 fi
 
 # Initialize Conda
 if [[ -x ~/miniconda3/bin/conda ]]; then
     echo "Initializing Conda..."
-    ~/miniconda3/bin/conda init "$(basename "$SHELL")"
     ~/miniconda3/bin/conda init bash
     ~/miniconda3/bin/conda init zsh
 
-    echo "Reloading the shell..."
-    if [[ $- == *i* ]]; then
-        source ~/.bashrc 2>/dev/null || source ~/.zshrc 2>/dev/null
-    else
-        echo "Please restart your terminal or run: source ~/.bashrc or source ~/.zshrc"
+    # Define file paths
+    BASHRC="$HOME/.bashrc"
+    BASH_PROFILE="$HOME/.bash_profile"
+
+    touch $BASHRC $BASH_PROFILE
+    
+    # Function to extract and copy the Conda block
+    copy_conda_block() {
+        local source_file=$1
+        local target_file=$2
+
+        # Extract the Conda block from the source file
+        CONDA_BLOCK=$(sed -n '/# >>> conda initialize >>>/,/# <<< conda initialize <<</p' "$source_file")
+
+        # Append the Conda block to the target file
+        echo "Adding Conda initialization block to $target_file."
+        echo ""
+        echo "$source_file // $target_file // $CONDA_BLOCK"
+        echo "" >> $target_file
+        echo  "$CONDA_BLOCK" >> "$target_file"
+        echo "Conda initialization block added to $target_file."
+    }
+
+    # Check for Conda block in both files
+    BASHRC_HAS_BLOCK=false
+    BASH_PROFILE_HAS_BLOCK=false
+
+    if grep -q "# >>> conda initialize >>>" "$BASHRC"; then
+        BASHRC_HAS_BLOCK=true
+    fi
+
+    if grep -q "# >>> conda initialize >>>" "$BASH_PROFILE"; then
+        BASH_PROFILE_HAS_BLOCK=true
     fi
 
-    if command -v conda &>/dev/null; then
-        echo "Miniconda installed and initialized successfully!"
+    # Handle the cases
+    if $BASHRC_HAS_BLOCK && ! $BASH_PROFILE_HAS_BLOCK; then
+        echo "Conda initialization block found in .bashrc but missing in .bash_profile."
+        copy_conda_block "$BASHRC" "$BASH_PROFILE"
+    elif $BASH_PROFILE_HAS_BLOCK && ! $BASHRC_HAS_BLOCK; then
+        echo "Conda initialization block found in .bash_profile but missing in .bashrc."
+        copy_conda_block "$BASH_PROFILE" "$BASHRC"
+    elif $BASHRC_HAS_BLOCK && $BASH_PROFILE_HAS_BLOCK; then
+        echo "Conda initialization block already exists in both .bashrc and .bash_profile. No changes made."
     else
-        echo "Miniconda installation succeeded but initialization failed. Please check your shell configuration."
+        echo "No Conda initialization block found in either .bashrc or .bash_profile."
+        echo "From a bash shell, please run 'conda init bash' to initialize Conda."
+        exit 1
     fi
+
+    echo "Miniconda installation successful."
+    echo "Open a new shell, and conda should be available (try: 'conda -v')."
 else
-    echo "Miniconda installation failed. Please try again."
-    return 3
+    echo "Miniconda installation failed. Please try again and/or atttempt the commands in this script manually."
+    exit 3
 fi
diff --git a/bin/other/regsub_yaml.sh b/bin/other/regsub_yaml.sh
index d3f174e9..ccc57b0f 100755
--- a/bin/other/regsub_yaml.sh
+++ b/bin/other/regsub_yaml.sh
@@ -33,4 +33,6 @@ while IFS='=' read -r key value; do
     sed -i "" "s/$key/$escaped_value/g" "$cluster_cfg_yaml"
 done < "$cluster_init_values"
 
-echo "\n\n\tSubstitutions completed in $cluster_cfg_yaml.\n"
+echo "" 
+echo "Substitutions completed in $cluster_cfg_yaml."
+echo ""
diff --git a/bin/retshell b/bin/retshell
new file mode 100644
index 00000000..5a43d324
--- /dev/null
+++ b/bin/retshell
@@ -0,0 +1,2 @@
+CURR_SHELL=$(ps -p $$ -o comm=)
+echo "$CURR_SHELL"
\ No newline at end of file
diff --git a/config/day/daycli.yaml b/config/day/daycli.yaml
index f90c4d05..e1b87905 100755
--- a/config/day/daycli.yaml
+++ b/config/day/daycli.yaml
@@ -19,6 +19,8 @@ dependencies:
   - tabix
   - fd-find
   - graphviz
+  - nodejs
+  - jq
   - pip:
     - docopt==0.6.2
     - colr==0.9.1
diff --git a/docs/quickest_start.md b/docs/quickest_start.md
index 171c5818..c7ba410f 100644
--- a/docs/quickest_start.md
+++ b/docs/quickest_start.md
@@ -24,10 +24,10 @@ _on the laptop you'll create ephemeral cluster, where you have saved the daylily
 _One is needed per region you intend to run in._
 
 ```bash
-AWS_PROFILE=daylily-service
+export AWS_PROFILE=daylily-service
 BUCKET_PREFIX=yocorp
 REGION=us-west-2
-bash ./bin/create_daylily_omics_analysis_s3.sh  --disable-warn --region $REGION --profile $AWS_PROFILE --bucket-prefix $BUCKET_PREFIX --disable-dryrun
+./bin/create_daylily_omics_analysis_s3.sh  --disable-warn --region $REGION --profile $AWS_PROFILE --bucket-prefix $BUCKET_PREFIX --disable-dryrun
 ```
 
 - This will take ~20min if you remain in `us-west-2`, longer if cross region.
@@ -45,7 +45,7 @@ rclone copy $sentieon_lic yocorp_remote:yocorp-daylily-omics-analysis-us-west-2/
 ### Check Spot Market Pricing (optional, but suggested to get best pricing over time)
 
 ```bash
-AWS_PROFILE=daylily-service
+export AWS_PROFILE=daylily-service
 REGION=us-west-2          
 OUT_TSV=./init_daylily_cluster.tsv
 
@@ -57,11 +57,11 @@ OUT_TSV=./init_daylily_cluster.tsv
 ### Create Ephemeral Cluster
 _this script will check and install a number of prerequsites and attempt to install_
 
-```zsh
-AWS_PROFILE=daylily-service
+```bash
+export AWS_PROFILE=daylily-service
 REGION_AZ=us-west-2c
 
-source bin/daylily-create-ephemeral-cluster --region-az $REGION_AZ --profile $AWS_PROFILE
+./bin/daylily-create-ephemeral-cluster --region-az $REGION_AZ --profile $AWS_PROFILE
 ```
 
 You will be prompted for a variety of config settings. Some resources, if missing, will be created. Other resources if missing will trigger failures.  If all is well, you'll be left with a success message with a suggested command to start a remote test on the headnode.
diff --git a/setup.py b/setup.py
index 9637008c..6bfd9a6d 100755
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name="daylily",
-    version="0.7.155",
+    version="0.7.156",
     packages=find_packages(),
     install_requires=[
         # Add dependencies here