QIIME2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed, see https:\/\/qiime2.org\/<\/a><\/p>\n To use the install already available, see below. As a central install, users cannot write to the QIIME2 conda environment (if they wanted to add their own packages).<\/p>\n There is an older version of QIIME2, also available:<\/p>\n If you’d like to install your own version that you can modify, you can run:<\/p>\n You’ll just need this bit to use your personal qiime2 install in a jobscript in the future:<\/p>\n Here is an 8 core job, using a central install as an example:<\/p>\n Overview QIIME2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed, see https:\/\/qiime2.org\/ Set up procedure Central install To use the install already available, see below. Do -not- run any heavy lifting on the login nodes, instead submit a batch job. 2021.11 module load apps\/anaconda3\/5.2.0\/bin source \/opt\/apps\/apps\/python\/conda_init\/conda_init_bash.sh conda activate \/opt\/apps\/apps\/python\/qiime2\/2021.11 qiime info 2021.4 module load apps\/anaconda3\/5.2.0\/bin source \/opt\/apps\/apps\/python\/conda_init\/conda_init_bash.sh conda activate \/opt\/apps\/apps\/python\/qiime2\/2021.4 qiime info As a central install, users cannot.. Read more »<\/a><\/p>\n","protected":false},"author":14,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-5514","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5514","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/14"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=5514"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5514\/revisions"}],"predecessor-version":[{"id":6513,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5514\/revisions\/6513"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=5514"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Set up procedure<\/h2>\n
Central install<\/h3>\n
\nDo -not- run any heavy lifting on the login nodes, instead submit a batch job.<\/p>\n2021.11<\/h3>\n
module load apps\/anaconda3\/5.2.0\/bin\r\nsource \/opt\/apps\/apps\/python\/conda_init\/conda_init_bash.sh\r\nconda activate \/opt\/apps\/apps\/python\/qiime2\/2021.11\r\nqiime info<\/pre>\n
2021.4<\/h3>\n
module load apps\/anaconda3\/5.2.0\/bin\r\nsource \/opt\/apps\/apps\/python\/conda_init\/conda_init_bash.sh\r\nconda activate \/opt\/apps\/apps\/python\/qiime2\/2021.4\r\nqiime info<\/pre>\n
module load apps\/qiime2\/2019.1.0\/bin<\/pre>\n
Local install<\/h3>\n
qrsh -l short\r\nmodule load apps\/python\/miniconda3\/4.10.3\r\nconda config --set auto_activate_base false\r\nmodule load tools\/env\/proxy\r\nwget https:\/\/data.qiime2.org\/distro\/core\/qiime2-2022.8-py38-linux-conda.yml\r\nhttp_proxy=http:\/\/proxy.man.ac.uk:3128\r\nhttps_proxy=http:\/\/proxy.man.ac.uk:3128\r\nmkdir -p \/scratch\/$USER\/qiime2\/2022.8\r\nconda env create --prefix=\/scratch\/$USER\/qiime2\/2022.8 --file qiime2-2022.8-py38-linux-conda.yml # takes ~1 hour \r\nrm qiime2-2022.8-py38-linux-conda.yml # optional cleanup\r\nconda activate qiime2-2022.8 \r\nqiime info<\/pre>\n
module load apps\/anaconda3\/5.2.0\/bin\r\nsource \/opt\/apps\/apps\/python\/conda_init\/conda_init_bash.sh\r\nconda activate qiime2-2022.8<\/pre>\n
Example parallel job<\/h3>\n
#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe smp.pe 8 # Number of cores (can be 2--24)\r\n#$ -N ASV-DADA2 # Give the job a name\r\n\r\n# Input 1: single end Illumina sequences (.fastq)\r\n# Input 2: Manifest file (sequences.tsv) validated with keemei \r\n\r\nmodule load apps\/anaconda3\/5.2.0\/bin \r\nsource \/opt\/apps\/apps\/python\/conda_init\/conda_init_bash.sh \r\nconda activate \/opt\/apps\/apps\/python\/qiime2\/2021.4\r\n\r\n# Import sequences\r\n\r\nqiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sequences.tsv --output-path sequences.qza --input-format SingleEndFastqManifestPhred33V2\r\n\r\n# Denoise with DADA2\r\n\r\nqiime dada2 denoise-single --i-demultiplexed-seqs sequences.qza --p-trim-left 0 --p-trunc-len 251 --o-representative-sequences rep-seqs.qza --o-table table.qza --o-denoising-stats stats-dada2.qza\r\nqiime feature-table summarize --i-table table.qza --o-visualization table.qzv\r\nqiime metadata tabulate --m-input-file stats-dada2.qza --o-visualization stats-dada2.qzv\r\nqiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv\r\n\r\n# Taxnomic asignation\r\nqiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza\r\nqiime metadata tabulate --m-input-file taxonomy.qza --o-visualization taxonomy.qzv\r\nqiime taxa barplot --i-table table.qza --i-taxonomy taxonomy.qza --m-metadata-file metadata.tsv --o-visualization taxa-bar-plots.qzv\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"