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        "description": "# NRC-LIMS-dataDownloader\n\n\n## Description\n\nNRC-LIMS-Datadownloader is a software written in Python. This software explores the NRC-LIMS website, downloads all the sequence files, and keeps the meta data of all the sequences in a sqlite database.\n\nThe list of the tasks performed by the software:\n1. Scrapes the NRC-LIMS website to get a list of all the completed sequence runs and all information related to sequence runs and sequence files.\n2. Obtains new runs that were not been previously downloaded or re-processed/modified runs by checking each sequence run against the database.\n3. Download each new/re-processed run's data and subsequently unzips the file to obtain demultiplexed fastq files\n4. Renames each fastq file to the submitted sample name from the sequencing run information page.\n5. Generates a SHA256 code for each fastq file and gzips the file\n6. Inserts information about newly downlaoded runs and files into database\n\n\n## Requirements\n\n* Python 2.7\n* VirtualEnv\n* GNU Make\n\n\n## Deployment Procedures\n\n* Create and start the virtual enviroment \n    > cd path/to/your/folder  \n    > virtualenv -p /path/to/python2.7 venv  \n    > source venv/bin/activate  \n\n* Install the program and all the dependencies\n    > pip install nrc_ngs_dl \n \n* Copy the sample configuration file _config.ini.sample_ to _config.ini_ and provide the required settings\n    > cp venv/bin/config.ini.sample config.ini    \n    > vim config.ini  \n \n* Run the program\n    > cd path/to/your/folder  \n    > source venv/bin/activate  \n    > lims_downloader -c config.ini  \n\n\n## Set up the HCRON service\n\n* Get the permission to access hcron1.science.gc.ca by opening an IT centre ticket with message:\n    > HPC Dorval - Supercomputing - DC000131  \n    > Please register my account   chz001   to use hcron on:  \n    > hcron1.science.gc.ca  \n\n* Setup Passwordless Login\n    > https://portal.science.gc.ca/confluence/display/SCIDOCS/SSH+Login+without+a+Password    \n    > mkdir -p ~/.ssh  \n    > chmod -R 700 ~/.ssh    \n    > cd ~/.ssh  \n    > ssh-keygen -q -t rsa  \n    > cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_key   \n\n* Create the home for your hcron events:\n    > bash-4.1$ mkdir -p  ~/.hcron/hcron1.science.gc.ca/events\n\n* Create a hcron event file (file downloader as an example) :\n    > bash-4.1$ cd ~/.hcron/hcron1.science.gc.ca/events  \n    > bash-4.1$ hcron-event downloader  \n\n* Configure the event file to run the program nightly (file downloader as an example):\n    > bash-4.1$ cat ~/.hcron/hcron1.science.gc.ca/events/downloader   \n    > as_user=  \n    > host=142.135.29.204  \n    > command=bash -l -c /space/project/grdi/eco/groups/mbb/chz001/dataDownloader/hcron_command.sh  \n    > notify_email=chunfang.zheng@canada.ca  \n    > notify_message=message from hcron  \n    > when_month=*  \n    > when_day=*  \n    > when_hour=2  \n    > when_minute=0  \n    > when_dow=*  \n    > template_name=  \n    > bash-4.1$ \n\n* Command file(hcron_command.sh)\n    > bash-4.1$ cat /space/project/grdi/eco/groups/mbb/chz001/dataDownloader/hcron_command.sh   \n    > #!/bin/bash  \n    > echo \"start at `date`\" >> $HOME/check_step  \n    > cd /space/project/grdi/eco/groups/mbb/chz001/dataDownloader  \n    > source venv/bin/activate  \n    > lims_downloader -c config.ini  \n    > echo \"end at `date`\" >> $HOME/check_step \n\n* Getting Your Environment Right\n    > from https://expl.info/display/HCRON/Getting+Your+Environment+Right    \n    > \"The brute force way is to run a shell as a login shell, which will provide an environment almost equivalent to an interactive session\"   \n    > command=bash -l -c \"<commands here>\"   \n    > note: from my test, the trick works for host=142.135.29.204, but not for host=gpsc-in.science.gc.ca  \n\n* Connect to hcron server\n    > bash-4.1$ ssh hcron1.science.gc.ca\n\n* Load your hcron events\n    > chz001@hcron1: hcron-reload\n\n\n## SQLite database\n\nThree tables are maintained in this database. Tables will be updated when the program is run.\n\n1. data_packages: to keep all the information about each sequence run\n (run-name,....)\n2. data_files: to keep all the information about each sequence file, \ninclude information scrapped from webpage, checksum(SHA256), original name and new name of the file, etc. \n3. program_action: to keep all the information of every time the application is run,\n  like failures, successes, urls scraped/attempted, timestamps, sequence runs downloaded.",
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