diff --git a/apps/alakazam/4.1/common/aa_properties.R b/apps/alakazam/4.1/common/aa_properties.R
new file mode 100755
index 0000000..7effef2
--- /dev/null
+++ b/apps/alakazam/4.1/common/aa_properties.R
@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+
+# Alakazam AA properties
+#
+# Author: Scott Christley
+# Date: Sep 3, 2020
+# 
+
+# based upon this script for parsing args with optparse
+# https://bitbucket.org/kleinstein/immcantation/src/master/pipelines/shazam-threshold.R
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("alakazam"))
+suppressPackageStartupMessages(library("airr"))
+
+# Define commmandline arguments
+opt_list <- list(make_option(c("-d", "--db"), dest="DB",
+                             help="Tabulated data file, in AIRR format (TSV)."),
+                 make_option(c("-t", "--trim"), dest="TRIM", default=FALSE,
+                             help=paste("Trim conserved residues.",
+                                        "\n\t\tDefaults to FALSE.")),
+
+# Parse arguments
+opt <- parse_args(OptionParser(option_list=opt_list))
+
+# Check input file
+if (!("DB" %in% names(opt))) {
+    stop("You must provide a database file with the -d option.")
+}
+
+# Read rearrangement data
+db <- airr::read_rearrangement(opt$DB)
+
+aa_db <- aminoAcidProperties(db, seq="junction_aa", label="junction")
+
+airr::write_rearrangement(aa_db, 'aa_properties.airr.tsv')
diff --git a/apps/alakazam/4.1/common/alakazam_common.sh b/apps/alakazam/4.1/common/alakazam_common.sh
new file mode 100644
index 0000000..c4945b7
--- /dev/null
+++ b/apps/alakazam/4.1/common/alakazam_common.sh
@@ -0,0 +1,96 @@
+#
+# Alakazam common functions
+#
+# This script relies upon global variables
+# source alakazam_common.sh
+#
+# Author: Scott Christley
+# Date: Aug 17, 2020
+# 
+
+# required global variables:
+# PYTHON
+# AGAVE_JOB_ID
+# and...
+# The agave app input and parameters
+
+# the app
+export APP_NAME=alakazam
+
+# ----------------------------------------------------------------------------
+function expandfile () {
+    fileBasename="${1%.*}" # file.txt.gz -> file.txt
+    fileExtension="${1##*.}" # file.txt.gz -> gz
+
+    if [ ! -f $1 ]; then
+        echo "Could not find input file $1" 1>&2
+        exit 1
+    fi
+
+    if [ "$fileExtension" == "gz" ]; then
+        gunzip $1
+        export file=$fileBasename
+        # don't archive the intermediate file
+    elif [ "$fileExtension" == "bz2" ]; then
+        bunzip2 $1
+        export file=$fileBasename
+    elif [ "$fileExtension" == "zip" ]; then
+        unzip -o $1
+        export file=$fileBasename
+    else
+        export file=$1
+    fi
+}
+
+# prevent Agave from archiving the file
+function noArchive() {
+    echo $1 >> .agave.archive
+}
+
+# ----------------------------------------------------------------------------
+# Analysis provenance
+function initProvenance() {
+    # nothing yet
+    echo "initProvenance"
+}
+
+# ----------------------------------------------------------------------------
+# Workflow
+
+function print_versions() {
+    echo "VERSIONS:"
+    singularity exec ${singularity_image} versions report
+    echo -e "\nSTART at $(date)"
+}
+
+function print_parameters() {
+    echo "Input files:"
+    echo "singularity_image=${singularity_image}"
+    echo "metadata_file=${metadata_file}"
+    echo "rearrangement_file=${rearrangement_file}"
+    echo ""
+    echo "Application parameters:"
+    echo "gene_usage_flag=${gene_usage_flag}"
+    echo "aa_properties_flag=${aa_properties_flag}"
+    echo "aa_properties_trim=${aa_properties_trim}"
+}
+
+function run_alakazam_workflow() {
+    initProvenance
+
+    # expand rearrangement file if its compressed
+    expandfile $rearrangement_file
+    noArchive $file
+
+    # Gene Usage
+    if [[ $gene_usage_flag -eq 1 ]]; then
+        singularity exec -B $PWD:/data ${singularity_image} /data/gene_usage.R -d $file
+    fi
+
+    # Amino Acid properties
+    if [[ $aa_properties_flag -eq 1 ]]; then
+        # run it
+        singularity exec -B $PWD:/data ${singularity_image} /data/aa_properties.R -d $file
+    fi
+
+}
diff --git a/apps/alakazam/4.1/common/gene_usage.R b/apps/alakazam/4.1/common/gene_usage.R
new file mode 100755
index 0000000..a05fe56
--- /dev/null
+++ b/apps/alakazam/4.1/common/gene_usage.R
@@ -0,0 +1,59 @@
+#!/usr/bin/env Rscript
+
+# Alakazam gene usage
+#
+# Author: Scott Christley
+# Date: Sep 3, 2020
+# 
+
+# based upon this script for parsing args with optparse
+# https://bitbucket.org/kleinstein/immcantation/src/master/pipelines/shazam-threshold.R
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("alakazam"))
+suppressPackageStartupMessages(library("airr"))
+
+# Define commmandline arguments
+opt_list <- list(make_option(c("-d", "--db"), dest="DB",
+                             help="Tabulated data file, in AIRR format (TSV)."))
+
+# Parse arguments
+opt <- parse_args(OptionParser(option_list=opt_list))
+
+# Check input file
+if (!("DB" %in% names(opt))) {
+    stop("You must provide a database file with the -d option.")
+}
+
+# Read rearrangement data
+db <- airr::read_rearrangement(opt$DB)
+
+# allele
+genes <- countGenes(db, gene='v_call', group='repertoire_id', mode='allele', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='v_allele_usage.tsv')
+genes <- countGenes(db, gene='d_call', group='repertoire_id', mode='allele', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='d_allele_usage.tsv')
+genes <- countGenes(db, gene='j_call', group='repertoire_id', mode='allele', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='j_allele_usage.tsv')
+# TODO: Alakazam throws an error and stops execution if no data in c_call field
+# We need to figure out to check for this
+#genes <- countGenes(db, gene='c_call', group='repertoire_id', mode='allele', copy='duplicate_count', fill=T)
+#write.table(genes, row.names=F, sep='\t', file='c_allele_usage.tsv')
+
+# gene
+genes <- countGenes(db, gene='v_call', group='repertoire_id', mode='gene', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='v_gene_usage.tsv')
+genes <- countGenes(db, gene='d_call', group='repertoire_id', mode='gene', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='d_gene_usage.tsv')
+genes <- countGenes(db, gene='j_call', group='repertoire_id', mode='gene', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='j_gene_usage.tsv')
+#genes <- countGenes(db, gene='c_call', group='repertoire_id', mode='gene', copy='duplicate_count')
+#write.table(genes, row.names=F, sep='\t', file='c_gene_usage.tsv')
+
+# family/subgroup
+genes <- countGenes(db, gene='v_call', group='repertoire_id', mode='family', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='v_subgroup_usage.tsv')
+genes <- countGenes(db, gene='d_call', group='repertoire_id', mode='family', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='d_subgroup_usage.tsv')
+genes <- countGenes(db, gene='j_call', group='repertoire_id', mode='family', copy='duplicate_count')
+write.table(genes, row.names=F, sep='\t', file='j_subgroup_usage.tsv')
diff --git a/apps/alakazam/4.1/ls5/alakazam.json b/apps/alakazam/4.1/ls5/alakazam.json
new file mode 100644
index 0000000..073cb3e
--- /dev/null
+++ b/apps/alakazam/4.1/ls5/alakazam.json
@@ -0,0 +1,236 @@
+{
+  "name": "irplus-alakazam-ls5",
+  "version": "4.1",
+  "label": "alakazam",
+  "defaultQueue": "normal",
+  "defaultNodeCount": 1,
+  "defaultProcessorsPerNode": 40,
+  "defaultRequestedTime": "1:00:00",
+  "shortDescription": "Alakazam app on Lonestar5",
+  "longDescription": "iReceptor+ Alakazam app",
+  "executionType": "HPC",
+  "executionSystem": "irplus-ls5.tacc.utexas.edu",
+  "parallelism": "PARALLEL",
+  "checkpointable": false,
+  "deploymentPath": "/irplus/apps/alakazam/4.1/ls5/",
+  "deploymentSystem": "data.vdjserver.org",
+  "templatePath": "alakazam.sh",
+  "testPath": "test/test.sh",
+  "ontology": [
+    "http://sswapmeet.sswap.info/agave/apps/Application"
+  ],
+  "modules": [
+    "purge",
+    "load TACC"
+  ],
+  "inputs": [
+    {
+      "id": "singularity_image",
+      "details": {
+        "label": "",
+        "description": "Singularity image file",
+        "showAttribute": false
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "http://sswapmeet.sswap.info/mime/application/Json"
+        ],
+        "fileTypes": [
+          "text-0"
+        ]
+      },
+      "value": {
+        "default": "",
+        "visible": true,
+        "required": true
+      }
+    },
+    {
+      "id": "metadata_file",
+      "details": {
+        "label": "",
+        "description": "AIRR Repertoire metadata file",
+        "showAttribute": false
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "http://sswapmeet.sswap.info/mime/application/Json"
+        ],
+        "fileTypes": [
+          "text-0"
+        ]
+      },
+      "value": {
+        "default": "",
+        "visible": true,
+        "required": true
+      }
+    },
+    {
+      "id": "rearrangement_file",
+      "details": {
+        "label": "",
+        "description": "Rearrangement AIRR TSV file",
+        "showAttribute": false
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "http://sswapmeet.sswap.info/mime/application/Json"
+        ],
+        "fileTypes": [
+          "text-0"
+        ]
+      },
+      "value": {
+        "default": "",
+        "visible": true,
+        "required": true
+      }
+    }
+  ],
+  "parameters": [
+    {
+      "id": "creator",
+      "value": {
+        "visible": true,
+        "required": true,
+        "type": "string",
+        "default": ""
+      },
+      "details": {
+        "label": "Creator",
+        "description": "Username that created this job."
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "xsd:string"
+        ]
+      }
+    },
+    {
+      "id": "gene_usage_flag",
+      "value": {
+        "visible": true,
+        "required": true,
+        "type": "bool",
+        "order": 0,
+        "enquote": false,
+        "default": false,
+        "validator": null
+      },
+      "details": {
+        "label": "",
+        "description": "Calculate gene usage",
+        "argument": null,
+        "showArgument": false,
+        "repeatArgument": false
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "xsd:boolean"
+        ]
+      }
+    },
+    {
+      "id": "aa_properties_flag",
+      "value": {
+        "visible": true,
+        "required": true,
+        "type": "bool",
+        "order": 0,
+        "enquote": false,
+        "default": false,
+        "validator": null
+      },
+      "details": {
+        "label": "",
+        "description": "Calculate amino acid properties",
+        "argument": null,
+        "showArgument": false,
+        "repeatArgument": false
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "xsd:boolean"
+        ]
+      }
+    },
+    {
+      "id": "aa_properties_trim",
+      "value": {
+        "visible": true,
+        "required": false,
+        "type": "bool",
+        "order": 0,
+        "enquote": false,
+        "default": false,
+        "validator": null
+      },
+      "details": {
+        "label": "",
+        "description": "Trim parameter for calculate amino acid properties",
+        "argument": null,
+        "showArgument": false,
+        "repeatArgument": false
+      },
+      "semantics": {
+        "minCardinality": 1,
+        "maxCardinality": 1,
+        "ontology": [
+          "xsd:boolean"
+        ]
+      }
+    },
+    {
+      "id": "optional_number",
+      "value": {
+        "visible": true,
+        "required": false,
+        "type": "number"
+      },
+      "details": {
+        "label": "",
+        "description": "Optional number parameter"
+      },
+      "semantics": {
+        "minCardinality": 0,
+        "maxCardinality": 1,
+        "ontology": [
+          "xsd:integer"
+        ]
+      }
+    },
+    {
+      "id": "optional_enum",
+      "value": {
+        "visible": true,
+        "required": false,
+        "type": "enumeration",
+        "enumValues": [ "allele", "gene" ]
+      },
+      "details": {
+        "label": "",
+        "description": "Optional enum parameter"
+      },
+      "semantics": {
+        "minCardinality": 0,
+        "maxCardinality": 1,
+        "ontology": [
+          "xsd:string"
+        ]
+      }
+    }
+  ]
+}
diff --git a/apps/alakazam/4.1/ls5/alakazam.sh b/apps/alakazam/4.1/ls5/alakazam.sh
new file mode 100644
index 0000000..d358f1f
--- /dev/null
+++ b/apps/alakazam/4.1/ls5/alakazam.sh
@@ -0,0 +1,73 @@
+#
+# wrapper script
+# for Lonestar5
+# 
+
+# Configuration settings
+
+# These get set by Tapis
+
+# input files
+singularity_image="${singularity_image}"
+metadata_file="${metadata_file}"
+rearrangement_file="${rearrangement_file}"
+
+# application parameters
+gene_usage_flag=${gene_usage_flag}
+aa_properties_flag="${aa_properties_flag}"
+aa_properties_trim="${aa_properties_trim}"
+
+# Agave info
+AGAVE_JOB_ID=${AGAVE_JOB_ID}
+AGAVE_JOB_NAME=${AGAVE_JOB_NAME}
+AGAVE_LOG_NAME=${AGAVE_JOB_NAME}-${AGAVE_JOB_ID}
+
+# ----------------------------------------------------------------------------
+# unpack local executables
+#tar zxf binaries.tgz
+
+chmod +x gene_usage.R
+chmod +x aa_properties.R
+
+# modules
+module load python3
+module load launcher/3.4
+module load tacc-singularity
+
+PYTHON=python3
+
+export PATH="$PWD/bin:${PATH}"
+export PYTHONPATH=$PWD/lib/python3.7/site-packages:$PYTHONPATH
+
+# bring in common functions
+source ./alakazam_common.sh
+
+# ----------------------------------------------------------------------------
+# Launcher to use multicores on node
+export LAUNCHER_WORKDIR=$PWD
+export LAUNCHER_LOW_PPN=1
+export LAUNCHER_MID_PPN=8
+export LAUNCHER_MAX_PPN=25
+export LAUNCHER_PPN=1
+export LAUNCHER_JOB_FILE=joblist
+export LAUNCHER_SCHED=interleaved
+
+# Start
+printf "START at $(date)\n\n"
+
+# If you want to tell Tapis that the job failed
+export JOB_ERROR=0
+
+print_parameters
+print_versions
+run_alakazam_workflow
+
+# End
+printf "DONE at $(date)\n\n"
+
+# remove binaries before archiving 
+rm -rf bin lib
+
+if [[ $JOB_ERROR -eq 1 ]]; then
+    ${AGAVE_JOB_CALLBACK_FAILURE}
+fi
diff --git a/apps/alakazam/4.1/ls5/test/test-aa-properties.json b/apps/alakazam/4.1/ls5/test/test-aa-properties.json
new file mode 100644
index 0000000..5c2ebe6
--- /dev/null
+++ b/apps/alakazam/4.1/ls5/test/test-aa-properties.json
@@ -0,0 +1,18 @@
+{
+  "name":"aa_properties",
+  "appId": "irplus-alakazam-ls5-4.1",
+  "batchQueue": "normal",
+  "maxRunTime": "01:00:00",
+  "nodeCount": 1,
+  "archive": false,
+  "archiveSystem": "data.vdjserver.org",
+  "inputs": {
+    "singularity_image": "agave://data.vdjserver.org//irplus/images/immcantation_suite-4.1.0.sif",
+    "rearrangement_file": "agave://data.vdjserver.org//irplus/data/TCR/vdjserver1.airr.tsv.gz"
+  },
+  "parameters": {
+    "creator": "schristley",
+    "gene_usage_flag": false,
+    "aa_properties_flag": true
+  }
+}
diff --git a/apps/alakazam/4.1/ls5/test/test-app.json b/apps/alakazam/4.1/ls5/test/test-app.json
new file mode 100644
index 0000000..e45b95f
--- /dev/null
+++ b/apps/alakazam/4.1/ls5/test/test-app.json
@@ -0,0 +1,19 @@
+{
+  "name":"gene_usage",
+  "appId": "irplus-alakazam-ls5-4.1",
+  "batchQueue": "normal",
+  "maxRunTime": "01:00:00",
+  "nodeCount": 1,
+  "archive": false,
+  "archiveSystem": "data.vdjserver.org",
+  "inputs": {
+    "singularity_image": "agave://data.vdjserver.org//irplus/images/immcantation_suite-4.1.0.sif",
+    "metadata_file": "agave://data.vdjserver.org//irplus/data/TCR/vdjserver1-metadata.airr.json",
+    "rearrangement_file": "agave://data.vdjserver.org//irplus/data/TCR/vdjserver1.airr.tsv.gz"
+  },
+  "parameters": {
+    "creator": "schristley",
+    "gene_usage_flag": true,
+    "aa_properties_flag": false
+  }
+}
diff --git a/apps/alakazam/4.1/ls5/test/test.sh b/apps/alakazam/4.1/ls5/test/test.sh
new file mode 100644
index 0000000..e69de29
diff --git a/apps/alakazam/4.1/ls5/upload-bundle.sh b/apps/alakazam/4.1/ls5/upload-bundle.sh
new file mode 100644
index 0000000..f9d9a84
--- /dev/null
+++ b/apps/alakazam/4.1/ls5/upload-bundle.sh
@@ -0,0 +1,35 @@
+#
+TOOL=alakazam
+SYSTEM=ls5
+VER=4.1
+
+# Copy all of the object files to the bundle directory
+# and create a binaries.tgz
+#
+# For example:
+# cd bundle
+
+# tar zcvf binaries.tgz bin lib
+
+# delete old working area in tapis
+tapis files delete agave:///irplus/apps/$TOOL/$VER/$SYSTEM
+
+# create directory structure
+tapis files mkdir agave:///irplus/apps $TOOL
+tapis files mkdir agave:///irplus/apps/$TOOL $VER
+tapis files mkdir agave:///irplus/apps/$TOOL/$VER $SYSTEM
+tapis files mkdir agave:///irplus/apps/$TOOL/$VER/$SYSTEM test
+
+# upload app assets
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM alakazam.sh
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM alakazam.json
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM ../common/alakazam_common.sh
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM ../common/gene_usage.R
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM ../common/aa_properties.R
+tapis files list agave:///irplus/apps/$TOOL/$VER/$SYSTEM
+
+# upload test assets
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM/test test/test.sh
+tapis files upload agave:///irplus/apps/$TOOL/$VER/$SYSTEM/test test/test-app.json
+tapis files list agave:///irplus/apps/$TOOL/$VER/$SYSTEM/test
+