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Release 2.4

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@multimeric multimeric released this 03 Nov 05:32
· 7 commits to 2.4 since this release
v2.4.0
3b592c3

New in Cpipe 2.4

Installer

  • Created new installer which manages a full cpipe install from scratch in as little as 30 minutes by downloading assets stored in a Swift object store (NeCTAR)
  • The installer bundles most runtimes like Python, Perl, Groovy etc., ensuring Cpipe will run identically on different machines
  • This also means that Cpipe requires less software to be installed on the host machine
  • This process is managed by an install script in the root directory (./install.sh)
  • This process is documented in the install documentation

Run Script

  • Cpipe now has a central run script (./cpipe) which can be used to run most common cpipe commands, including run, test, manipulate batches, designs and metadata files.
  • The script is documented in the commands documentation

Documentation

  • Comprehensive documentation is now included in Cpipe, which is visible either in your local copies or on GitHub
  • The documentation covers installing, running, configuring and various other aspects to operating Cpipe
  • Have a look at the documentation index here

Docker support

  • Cpipe is now able to run in a docker container
  • Just clone the repo, copy in the swift_credentials.sh file (refer to the documentation for an explanation), and run docker build . and you can generate a Cpipe docker container

ALL Design

  • In line with new recommendations, we now encourage you to use the built-in ALL design instead of creating a gene list for your own analysis
  • This design will cover all official UCSC genes instead of limiting the analysis. This will save having to re-analyse the data in case your gene list expands

Configuration Changes

  • The bpipe.config file has moved to bpipe.config.template, which is copied to bpipe.config when your run the install. This prevents your bpipe.config settings from being overwritten when you pull never versions of Cpipe.
  • The bpipe.config has been rewritten to include a template for use with an HPC queue system (e.g. torque). This means you only need to remove one comment and specify your queue system and Cpipe should work with your system
  • Command names have been given to each command in the pipeline, meaning that their settings (wall time, RAM etc.) can be configured in bpipe.config using the relevant name. For example, "vep" for the VEP command.
  • The samples.txt file previously located in each batch directory has been renamed to config.batch.groovy to reflect that it can be used to change any Cpipe configuration settings for the batch
  • New JAVA_OPTS variable in config.groovy/config.batch.groovy for setting flags that should always be used for Java, for instance -noverify for certain versions of Java that dislike Groovy bytecode.

Miscellaneous Changes

  • The Cpipe directory has been restructured to place all reference data in data, all tools and runtimes in tools, and all installation tasks in tasks
  • Some un-needed files have been removed from Cpipe

Support

2.4 will receive continued support on the 2.4 branch of Cpipe. Unlike the dev branch, which will often contain broken developments versions of Cpipe, if you remain on the 2.4 branch and pull periodically you will keep up-to-date but without any breaking changes.

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