[{"_1":2,"_162":-5,"_163":-5},"loaderData",{"_3":4,"_18":19,"_25":26,"_141":142},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16,"_17":11},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","dockerRebrandTour","routes/_layout",{"_20":-5,"_21":22,"_23":11,"_24":22},"username","isAskGordonEnabled",true,"showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_129":-5,"_130":11,"_131":22,"_132":11,"_133":11,"_134":-5,"_135":11,"_136":-5,"_137":138,"_139":91,"_140":-7},"canonicalUrl","https://hub.docker.com/r/loopgenomics/loop-server/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","loopgenomics","reponame","loop-server","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":11,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2019-07-03T21:28:04.53515Z","description","dockerized loop server utilizing SGE to process various loopgenomics kits.","is_private","last_updated","2019-11-11T22:24:25.839907Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",310,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","The container will be used to process various kits provided by Loop Genomics (https://www.loopgenomics.com).\n\nMinimum System Requirements\n\n CPU: 32 cores (64 threads)\n RAM: 128G\n Storage: 2G\n Temporary Storage: 200G \n\nInstallation\n\npull the image into a local machine: \n\n docker pull loopgenomics/loop-server:1.0.0\n\nRun\n\nstart from obtaining the distributed LoopAnalysis package (LoopGenomics-2.1) through heeshin@loopgenomics.com:\n1. Unzip LoopGenomics-2.1.zip including \"LoopAnalysis\", \"jars\" and \"references\".\n2. Prepare \"data\", \"temp\" and \"result\" dirs (local volumes).\n For example, \n /mnt/temp to store intermediate files\n /mnt/results to store the final output files \n /mnt/data to store fastq files\n3. Create a container.\n LOOPGENOMICS=/path/of/LoopGenomics-2.1\n TEMP=/mnt \n docker run --hostname=loop-server \\\n -v $LOOPGENOMICS/LoopAnalysis:/root/LoopAnalysis \\\n -v $LOOPGENOMICS/jars:/root/jars \\\n -v $LOOPGENOMICS/references:/root/references \\\n -v $TEMP/results:/root/results \\\n -v $TEMP/data:/root/data \\\n -v $TEMP/temp:/root/temp \\\n -ti loopgenomics/loop-server:1.0.0\n \n \"/path/of/LoopGenomics-2.1\" is where you extracted \"LoopGenomics-2.1.zip\".\n The volumes (directories) will be linked to the directories in the container.\n\n4. The \"docker run\" command let you log in the container. In the container, go to \"/root\" dir in the docker container.\n If you do \"ls\", you will see the structure of directory. \n\n5. Prepare env.xml in the \"/root\" as shown below:\n \n 2.1\n \n /root/temp\n /root/results\n /root\n \n \n cluster\n 24\n \n \n \n6. Run pipeline \n in the container, run the command to create pipeline scripts at \"/root/temp/test1. \n java -jar /root/jars/LoopGenomicsPipeline-2.1.jar \\\n -env /root/env.xml \\ \n -runName SCC1 \\\n -read1 /root/data/16s/SSC/SSC-5minSPRI_S4_L001_R1_001_subset.fq.gz \\\n -read2 /root/data/16s/SSC/SSC-5minSPRI_S4_L001_R2_001_subset.fq.gz \\\n -task create \\\n -batchId 111 \\\n -kit 16S\n\n To run the created script, replace \"-task create\" with \"-task run\".\n \n\nRun 18S_ITS kit, \n\nplease download references :\n1. ensembl_fungi\nhttps://drive.google.com/open?id=1E8-dtGtk0kczYrqGJ5BBvRgxz_lmElxA\n2. silva-18S\nhttps://drive.google.com/open?id=1l567PDjzETBoVG2ST9na7sCoj8Zj3WTx\n3. Unite\nhttps://drive.google.com/open?id=1U5KvvFlHtxphDsbUcbYmW4aS2gnA7KlQ\n\nThen, extract those and move to ..../LoopGenomics-2.1/reference.\n\nYou would see those reference in your docker container:\n\n root@loop-server:~/references# ls\n UNITE ensembl-fungi references.csv silva-132-SSURef silva-18S\n\nThe command would be like this (please make sure the \"-kit\" option) :\n\n java -jar /root/jars/LoopGenomicsPipeline-2.1.jar -env /root/env.xml \\\n -read1 /root/data/LW/LW-DecQC_S1_L001_R1_001.fastq.gz \\\n -read2 /root/data/LW/LW-DecQC_S1_L001_R2_001.fastq.gz \\\n -task run -batchId 1 \n -kit 18S_ITS \n -runName my_18S_ITS_test\n\nTips\n\nThe \"docker run\" with the options \"-ti\" will let you create a container and login into the container. However, when you \"CTRL-D\" or \"exit\", the container will stop itself as well as all the jobs. There is a way to avoid the inconvenience. \nUsing the \"-d\" option while creating a loop-server container, the container can be running as a daemon.\n\nFor example,\n\n docker run --hostname=loop-server \\\n -v $LOOPGENOMICS/LoopAnalysis:/root/LoopAnalysis \\\n -v $LOOPGENOMICS/jars:/root/jars \\\n -v $LOOPGENOMICS/references:/root/references \\\n -v $TEMP/results:/root/results \\\n -v $TEMP/data:/root/data \\\n -v $TEMP/temp:/root/temp \\\n -ti -d loopgenomics/loop-server:1.0.0\n\nIt will let the container run in the background as a daemon. You are still in the local environment, not in the container.\nFor example,\n\n ~$ docker ps -a\n CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES\n 4ce7e48353c4 loopgenomics/loop-server:1.0.0 \"/root/loopgenomics_…\" 6 seconds ago Up 4 seconds peaceful_ritchie\n\n\nYou can access the container using \"docker exec\" without stopping the container as well as all the jobs running in the container.\nFor example, the following shows how to login the container with its name such as \"peaceful_ritchie\" and how to run the LoopAnalysis package:\n\n ~$ docker exec -ti peaceful_ritchie /bin/bash\n root@loop-server:/#~# java -jar /root/jars/LoopGenomicsPipeline-2.1.jar -env /root/env.xml -runName LW3 -read1 /root/data/16s/LW_DecQC_S1/LW- \n DecQC_S1_L001_R1_001.fastq.gz -read2 /root/data/16s/LW_DecQC_S1/LW-DecQC_S1_L001_R2_001.fastq.gz -task run -batchId 111 -kit 16S\n Kit : 16s\n task : run\n created ... /root/temp/LW3/scripts/demult.sh\n created ... /root/temp/LW3/scripts/dictread.sh\n created ... /root/temp/LW3/scripts/run.sh\n created ... /root/temp/LW3/scripts/dictsplit.sh\n created ... /root/temp/LW3/scripts/barcodehasher.sh\n created ... /root/temp/LW3/scripts/shortreadmap_sub.sh\n created ... /root/temp/LW3/scripts/dictread_sub.sh\n created ... /root/temp/LW3/scripts/samplestats.sh\n created ... /root/temp/LW3/scripts/classify_sub.sh\n created ... /root/temp/LW3/scripts/runstats.sh\n created ... /root/temp/LW3/scripts/collectout.sh\n created ... /root/temp/LW3/scripts/otuclassify.sh\n created ... /root/temp/LW3/scripts/classify.sh\n created ... /root/temp/LW3/scripts/shortreadmap.sh\n CMD : /bin/sh /root/temp/LW3/scripts/run.sh\n Your job 1 (\"b111demult\") has been submittedYour job-array 2.1-24:1 (\"b111bchash\") has been submittedYour job-array 3.1-24:1 (\"b111dictsplit\") has been \n submittedYour job-array 4.1-24:1 (\"b111dictread\") has been submitted\n\n\nAfter you exit the container, you can log in again and check the status of your job submitted in the container.\nHere is a way to check the status of your job without logging in the container. As shown below, you will see the status of your pipeline\nin your local environment.\n\n ~$ docker exec -ti peaceful_ritchie qstat \n job-ID prior name user state submit/start at queue slots ja-task-ID \n \"-----------------------------------------------------------------------------------------------------------------\"\n 1 0.50000 b111demult root r 07/08/2019 23:36:57 all.q@loop-server 16 \n 2 0.00000 b111bchash root hqw 07/08/2019 23:36:52 1 1-24:1\n 3 0.00000 b111dictsp root hqw 07/08/2019 23:36:55 1 1-24:1\n 4 0.00000 b111dictre root hqw 07/08/2019 23:36:58 1 1-24:1\n\nFinally, while creating the container, the \"results\" dir and \"temp\" dir were linked between your local volume and the container's volume.\nYou can see the final outputs in \"/mnt/results\" in your local environment. 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loopgenomics/loop-server

Tags for loopgenomics/loop-server