Individual tasks script

individual_tasks/send_task_azure.sh

+#!/bin/bash
+
+usage()
+{
+    echo ""
+    echo "USAGE:"
+    echo "$0 [OPTIONS] -s SAMPLEID -t TASKID -a AZURETASKNAME -j JOBID"
+    echo ""
+    echo "OPTIONS"
+    echo "   -s SAMPLEID"
+    echo "          [REQUIRED] Sample id (e.g. SL284406)."
+    echo "   -t TASKID"
+    echo "          [REQUIRED] ID of the task (e.g. 1_2)."
+    echo "   -a AZURETASKNAME"
+    echo "          [REQUIRED] Name for the task for Azure batch."
+    echo "   -j JOBID"
+    echo "          [REQUIRED] Azure batch job id where the task is being sent."
+    echo "   -u INTEGER"
+    echo "          Subset reads to test pipeline (to INTEGER)."
+    echo "   -c INTEGER"
+    echo "          Number of cores to use (INTEGER)."
+    echo "   -m"
+    echo "          Monitor RAM/CPU."
+    echo "   -h"
+    echo "          Print (this) help message."
+    echo ""
+}
+
+# # NEEDS LOGGING IN INTO BATCH ACCOUNT !!!
+# az batch account login --name forneruosysmedutvbatch \
+#     --resource-group for-neuro-sysmed-utv-compute
+# az batch pool create --id wgbs-v5-pool --vm-size standard_d8_v3 \
+#     --node-agent-sku-id "batch.node.ubuntu 18.04" \
+#     --image /subscriptions/5a9e26a0-6897-44d6-963e-fae2a2061f27/resourceGroups/FOR-NEURO-SYSMED-UTV-COMPUTE/providers/Microsoft.Compute/galleries/neurosysmed.img.gallery/images/wgbs-vs-imgdef/versions/1.5.0 \
+#     --target-dedicated-nodes 20
+#az batch job create --id wgbs-strategy-2 --pool-id wgbs-v5-pool
+
+#### PARSE CMD LINE
+
+task_id=
+azure_task_id=
+sample_id=
+azure_job_id=
+subset=0
+cores=1
+MONITOR=0
+
+while getopts ":s:t:a:j:u:c:h" opt; do
+    case ${opt} in 
+        s)
+            sample_id=$OPTARG
+            ;;
+        t)
+            task_id=$OPTARG
+            ;;
+        a)
+            azure_task_id=$OPTARG
+            ;;
+        j)
+            azure_job_id=$OPTARG
+            ;;
+        u)
+            subset=$OPTARG
+            ;;
+        m)
+            MONITOR=1
+            ;;
+        c)
+            cores=$OPTARG
+            ;;
+        h)
+            usage
+            exit 0
+            ;;
+        \?)
+            echo "[ERROR] Invalid option: -$OPTARG" >&2
+            echo "        (try $0 -h for help)"
+            exit 1
+            ;;
+        :)
+            echo "[ERROR] Option -$OPTARG requires an argument." >&2
+            echo "        (try $0 -h for help)"
+            exit 1
+            ;;
+    esac
+done
+
+if [[ "$task_id" == "" ]]; then
+    echo "[ERROR] Task id (-t option) is required."
+    exit 1
+fi
+if [[ "$sample_id" == "" ]]; then
+    echo "[ERROR] Sample id (-i option) is required."
+    exit 1
+fi
+if [[ "$azure_task_id" == "" ]]; then
+    echo "[ERROR] Azure task id (-a option) is required."
+    exit 1
+fi
+if [[ "$azure_job_id" == "" ]]; then
+    echo "[ERROR] Azure job id (-j option) is required."
+    exit 1
+fi
+
+subset_opt=""
+if [[ $subset > 0 ]]; then
+    subset_opt=" -u ${subset}"
+fi
+if [[ $cores > 1 ]]; then
+    subset_opt="${subset_opt} -c ${cores}"
+fi
+if [[ $MONITOR == 1 ]]; then
+    subset_opt="${subset_opt} -m"
+fi
+
+CMD_LINE="/bin/bash /fileshares/forneurosysmedutvcompute/wgbs-resources/wgbs-pipeline/individual_tasks/task.sh -s ${sample_id} -t ${task_id} -f${subset_opt} -i forneurosysmedutvcompute/wgbsfqdata -o forneurosysmedutvcompute/bs"
+#CMD_LINE="/bin/bash /fileshares/forneurosysmedutvcompute/wgbs-resources/wgbs-pipeline/individual_tasks/task.sh -s ${sample_id} -t ${task_id} -f${subset_opt} -i forneurosysmedutvcompute/wgbsfqdata -o forneurosysmedutvcompute/pref"
+
+# CREATE JSON
+tmp_json=$(mktemp /tmp/task.XXXXXX)
+echo "{" > $tmp_json
+echo "  \"id\": \"${azure_task_id}\"," >> $tmp_json
+echo "  \"commandLine\": \"${CMD_LINE}\"," >> $tmp_json
+echo "  \"userIdentity\": {" >> $tmp_json
+echo "    \"autoUser\": {" >> $tmp_json
+echo "      \"elevationLevel\": \"admin\"," >> $tmp_json
+echo "      \"scope\": \"pool\"" >> $tmp_json
+echo "    }," >> $tmp_json
+echo "    \"userName\": null" >> $tmp_json
+echo "  }" >> $tmp_json
+echo "}" >> $tmp_json
+
+az batch task create --json-file ${tmp_json} --job-id ${azure_job_id}
+
+
+
+

process_by_sampleid.sh

@@ -10,7 +10,7 @@ usage()
 {
     echo ""
     echo "USAGE:"
-    echo "process_by_sampleid.sh [OPTIONS] -s <SAMPLE_ID> -i <STORAGE_ACCT_FASTQ>/<FILESHARE_FASTQ> -o <STORAGE_ACCT_RESULTS>/<FILESHARE_RESULTS_PREFIX>"
+    echo "$0 [OPTIONS] -s <SAMPLE_ID> -i <STORAGE_ACCT_FASTQ>/<FILESHARE_FASTQ> -o <STORAGE_ACCT_RESULTS>/<FILESHARE_RESULTS_PREFIX>"
     echo "  - SAMPLE_ID: e.g. SL284409"
     echo "  - STORAGE_ACCT_FASTQ: e.g. forneurosysmedutvcompute"
     echo "  - FILESHARE_FASTQ: Name of the fileshare, e.g. wgbsfqdata"
@@ -39,7 +39,7 @@ usage()
     echo ""
     echo "For the results, a new fileshare will be created for the sample analysed, whose name will be a concatenation of the form <FILESHARE_RESULTS_PREFIX>-<SAMPLE_ID>. If the fileshare name exists and is not empty, the program will fail."
     echo ""
-    echo "EXAMPLE: process_by_sampleid.sh SL284405 forneurosysmedutvcompute/wgbsfqdata forneurosysmedutvcompute/prefix"
+    echo "EXAMPLE: $0 -s SL284405 -i forneurosysmedutvcompute/wgbsfqdata -o forneurosysmedutvcompute/prefix"
 }
 
 ###### PARSE CMDLINE