Tools for working with the Seven Bridges bioinformatics platform.
u0028003$ java -jar ~/Code/SBApps/target/ProjectDownloader-0.3.jar
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** Project Downloader: April 2021 **
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This tool downloads files from Seven Bridges Projects while maintaining their folder
structure via the fast, multi-threaded, aria2 download utility. Files already
downloaded are skipped so run iteratively as new files become available.
Options:
-l List visible Projects.
-p Project ID (division/projectName) to download.
Skip this option to just list the visible Projects.
-r Regular expressions to select particular Project file paths to download.
Comma delimited, no spaces, enclose in 'xxx', defaults to all.
-d Download Project files into this directory.
Skip this option to just list the files.
-c Path to your SB unified credentials file.
Defaults to ~/.sevenbridges/credentials
If it does not exist, fetch an authentication token https://tinyurl.com/sbtoken
Then use a text editor to create the ~/.sevenbridges/credentials file following
the format in https://tinyurl.com/sbcred, chmod 600 the file, and keep it safe.
-a Account credentials to load, defaults to 'default'.
-s Skip files that failed URL creation instead of exiting. These are typically
archived in Glacier. Use the SB web console to unarchive them, then rerun.
-e Path to the aria2 executable, see https://aria2.github.io to download and install.
Skip this option to set up a mock aria2 download.
Examples assuming ~/.sevenbridges/credentials exists:
List visible Projects:
java -Xmx1G -jar pathTo/ProjectDownloader_xxx.jar -l
List files in a particular Project:
java -Xmx1G -jar pathTo/ProjectDownloader_xxx.jar -p alana-welm/pdx
Test Project file path regexes:
java -Xmx1G -jar pathTo/ProjectDownloader_xxx.jar -p alana-welm/pdx
-r '.+bam,.+cram,.+bai,.+crai'
Download available alignment files:
java -Xmx1G -jar pathTo/ProjectDownloader_xxx.jar -p alana-welm/pdx -d ~/PdxProj
-r '.+bam,.+cram,.+bai,.+crai' -e ~/Aria2/1.35/bin/aria2c
Download all Project files skipping archived objects:
java -Xmx1G -jar pathTo/ProjectDownloader_xxx.jar -p alana-welm/pdx -d ~/PdxProj
-s -e ~/Aria2/1.35/bin/aria2c
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