wtsi-hgi/hgc-tools

Name: hgc-tools

Owner: Wellcome Trust Sanger Institute - Human Genetics Informatics

Description: Set of tools for working with Mercury capsules.

Created: 2013-04-18 10:05:35.0

Updated: 2014-04-10 10:01:10.0

Pushed: 2014-04-10 10:01:09.0

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Size: 412

Language: Haskell

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README

Set of tools for working with Mercury capsules.

– hgc-version: Creates a new version of a template.

Create a new version of a Mercury capsule based on the specified template.
Usage: hgc-version [Option...] template
                  --amend                  Amend the current capsule rather than creating a new one.
                  --clone-only             Only clone the template, don't start the capsule.
  -m MOUNT_POINT  --mount=MOUNT_POINT      Mount the specified resource into the capsule.
  -M              --major                  Create a major revision.
  -n NAME         --new-capsule=NAME       Create a capsule under a new name.
  -p PKGDIR       --pkgdir=PKGDIR          Use specified directory in place of the aura source package cache.
  -r REPOSITORY   --repository=REPOSITORY  Use the specified repository name (defaults to mercury.repo).
  -v              --verbose                Enable verbose output.
  -y              --publish                Automatically publish new capsule.

– hgc-deploy: Run a capsule based on an exising template (intended to be installed suid root).

    Launch a Mercury capsule.
    Usage: hgc-deploy [Option...] capsule
      -m RESOURCE    --mount=RESOURCE         Load the specified resource into the capsule.
      -r REPOSITORY  --repository=REPOSITORY  Use the specified repository name (defaults to mercury.repo).
      -t UNION_TYPE  --union-type=UNION_TYPE  Set the type of filesystem used to implement the union mount. Currently supported are aufs and overlayfs.
      -v             --verbose                Enable verbose output.
                     --retain-temp            Retain the temporary files under /tmp/hgc

Installation

 Prerequisites

First, install the Haskell compiler and the cabal Haskell package manager

• Linux (kernel >= 3.2, 3.8 recommended)
• ghc >= 7.6 [http://www.haskell.org/platform/linux.html]
• cabal >= 1.18

If you are installing cabal for the first time (or you have issues running the build commands), you may want to upgrade cabal (as well as Haskell core packages) itself to the latest version (to get the cabal sandbox command and avoid other incompatibility issues). You can install a new version of cabal in your home directory using:

bal update
bal install cabal-install
port PATH=$(echo ~/.cabal/bin):$PATH

Build and install

bal sandbox init
bal install --only-dependencies
bal configure 
do cabal install --prefix=/usr/local/hgc-tools

If you'd like users other than root to run hgc-deploy, it must be setuid root:

do chmod u+s /usr/local/hgc-tools/bin/hgc-deploy

The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads 'Copyright (c) 2005, 2007- 2009, 2011-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012' and a copyright statement that reads “Copyright (c) 2005-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012'.”