Cellranger

.gitignore

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+apps/cellranger/0.1/common/test/*

apps/cellranger/0.1/common/cellranger_common.sh

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+#
+# Toy common functions
+#
+# This script relies upon global variables
+# source toy_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=cellranger
+
+# ----------------------------------------------------------------------------
+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"
+}
+
+# ----------------------------------------------------------------------------
+# Toy workflow
+
+function print_versions() {
+    echo "VERSIONS:"
+    #echo "  $(DefineClones.py --version 2>&1)"
+    singularity exec ${singularity_image} cellranger --version
+    echo -e "\nSTART at $(date)"
+}
+
+function print_parameters() {
+    echo "Input files:"
+    echo "singularity_image=${singularity_image}"
+    echo "input_file=${input_file}"
+    echo "input_file=${input_csv}"
+    echo ""
+    echo "Application parameters:"
+    echo "single_flag=${single_flag}"
+    echo "optional_number=${optional_number}"
+    echo "optional_enum=${optional_enum}"
+}
+
+function run_cellranger_workflow() {
+    initProvenance
+
+    fileBasename=${input_file##*/}
+    # launcher job file
+    if [ -f joblist ]; then
+        echo "Warning: removing file 'joblist'.  That filename is reserved." 1>&2
+        rm joblist
+        touch joblist
+    fi
+    noArchive "joblist"
+
+    singularity exec cellranger4-bcl.sif cellranger mkfastq --id=tutorial_walk_through \
+    --run=${fileBasename%.tar.gz} \
+    --csv=${input_csv}
+
+        #ARGS="--format airr --act set --model ham --sym min --norm len --dist 0.165"
+        #if [ -n "$define_clones_mode" ]; then
+        #    ARGS="$ARGS --mode $define_clones_mode"
+        #fi
+        #if [ -n "$define_clones_nproc" ]; then
+        #    ARGS="$ARGS --nproc $define_clones_nproc"
+        #fi
+
+        # Define Clones
+        #if [[ $define_clones -eq 1 ]]; then
+        #    echo "DefineClones.py -d ${filename} -o ${fileOutname} $ARGS" >> joblist
+        #fi
+
+
+    # check number of jobs to be run
+    numJobs=$(cat joblist | wc -l)
+    export LAUNCHER_PPN=$LAUNCHER_LOW_PPN
+    if [ $numJobs -lt $LAUNCHER_PPN ]; then
+        export LAUNCHER_PPN=$numJobs
+    fi
+
+    # run launcher
+    #$LAUNCHER_DIR/paramrun
+
+    ls -l
+
+}

apps/cellranger/0.1/ls5/cellranger.json

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+{
+  "name": "irplus-cellranger-ls5-franasa",
+  "version": "0.1",
+  "label": "cellranger",
+  "defaultQueue": "normal",
+  "defaultNodeCount": 1,
+  "defaultProcessorsPerNode": 40,
+  "defaultRequestedTime": "1:00:00",
+  "shortDescription": "cellranger 4.0 on Lonestar5",
+  "longDescription": "iReceptor+ cellranger app",
+  "executionType": "HPC",
+  "executionSystem": "irplus-ls5.tacc.utexas.edu",
+  "parallelism": "PARALLEL",
+  "checkpointable": false,
+  "deploymentPath": "/irplus/apps/cellranger/franasa/ls5/",
+  "deploymentSystem": "data.vdjserver.org",
+  "templatePath": "cellranger.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": "input_file",
+      "details": {
+        "label": "",
+        "description": "Test file cellranger-tiny-bcl-1.2.0.tar.gz",
+        "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": "input_csv",
+      "details": {
+        "label": "",
+        "description": "csv file cellranger-tiny-bcl-simple-1.2.0.csv",
+        "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": "single_flag",
+      "value": {
+        "visible": true,
+        "required": true,
+        "type": "bool",
+        "order": 0,
+        "enquote": false,
+        "default": false,
+        "validator": null
+      },
+      "details": {
+        "label": "",
+        "description": "Boolean flag parameter",
+        "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"
+        ]
+      }
+    }
+  ]
+}

apps/cellranger/0.1/ls5/cellranger.sh

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+#
+# wrapper script
+# for Lonestar5
+#
+
+# Configuration settings
+
+# These get set by Tapis
+
+# input files
+singularity_image="${singularity_image}"
+input_file="${input_file}"
+input_csv="${input_csv}"
+
+# application parameters
+single_flag=${single_flag}
+optional_number="${optional_number}"
+optional_enum="${optional_enum}"
+
+# Agave info
+AGAVE_JOB_ID=${AGAVE_JOB_ID}
+AGAVE_JOB_NAME=${AGAVE_JOB_NAME}
+AGAVE_LOG_NAME=${AGAVE_JOB_NAME}-${AGAVE_JOB_ID}
+
+# ----------------------------------------------------------------------------
+# unpack tiny test folder
+tar -zxvf ${input_file}
+#cellranger-tiny-bcl-1.2.0.tar.gz
+
+
+# modules
+module load python3
+module load launcher/3.4
+module load tacc-singularity
+
+PYTHON=python3
+
+export PATH="$PWD/bin:${PATH}"
+export PYTHONPATH=$PWD/lib/python3.7/site-packages:$PYTHONPATH
+
+# bring in common functions
+source ./cellranger_common.sh
+
+# ----------------------------------------------------------------------------
+# Launcher to use multicores on node
+export LAUNCHER_WORKDIR=$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_cellranger_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