Changes between Version 22 and Version 23 of HPC_deploy


Ignore:
Timestamp:
2015-11-18T20:11:09+01:00 (9 years ago)
Author:
Pieter Neerincx
Comment:

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  • HPC_deploy

    v22 v23  
    1111* Deployment of bioinformatics software is handled by the bioinformaticians from the ''depad'' group.
    1212
    13 If you want to become part of the ''depad'' group [wiki:Contact contact the helpdesk].
     13If you want to join the ''depad'' group, please [wiki:Contact contact the helpdesk].
    1414The depad group uses [https://hpcugent.github.io/easybuild/ EasyBuild], which uses !EasyConfigs as recipes to enforce consistent, reproducible installations.
    1515In a nutshell an !EasyConfig deployment recipe can handle the following steps:
     
    5353* On our machines in {{{/apps/sources/EasyBuild/custom/}}} - Bleeding edge home made !EasyConfigs that were not yet committed to and pull-merged into the !GitHub repos.
    5454
    55 If there is not an easybuild file (.eb) on github and there is no eb file on the cluster (/apps/sources/EasyBuild/custom), we have to create one ourselves.
     55If there is no existing !EasyConfig, we have to create one ourselves.
    5656
    57 First an example of an custom !EasyBuild file created for deploying NGS_DNA pipeline on the cluster. Below the code there will be the explanation of all the steps in the script.
     57First an example of an custom !EasyBuild file created for deploying our NGS_DNA pipeline. Below the code there will be the explanation of all the steps in the script.
    5858{{{
    5959name = 'NGS_DNA'
     
    9191 * All the installed eb configs are put automatically in the /apps/modules/all folder, but with '''moduleclass''' you can specify an extra module path.  '''N.B.''''''' when typing the command module avail on the cluster will only display the non-all modules. So specifying an extra moduleclass is necessary to find your module back in module avail  [[BR]]
    9292
    93 For installing more advanced tools like R please read the [https://hpcugent.github.io/easybuild/ documentation] online or have a look in our custom scripts on the cluster
     93For more complicated installations like for example for ''R'', please read the [https://hpcugent.github.io/easybuild/ documentation] online and have a look at existing !EasyConfigs.
    9494
    95 === installing a new tool ===
    96  * Create YOURFILE.eb file in /apps/sources/EasyBuild/custom/
     95=== Installing the software ===
     96 * Create a MyEasyConfig-1.2.3.eb file in {{{/apps/sources/EasyBuild/custom/}}}
    9797 * module load !EasyBuild
    98  * eb YOURFILE.eb
     98 * eb --robot --robot-paths=:/apps/sources/EasyBuild/custom/ /path/to/MyEasyConfig-1.2.3.eb
    9999
    100 Before you can execute the installed !EasyBuild file the module needs to be synced to the storage and nodes:
     100=== Updating the Lmod caches and syncing installed software to nodes ===
     101
     102Before you can use the installed software it needs to be synced to various places and the Lmod caches needs to be updated:
    101103{{{
    102104sudo -u umcg-envsync bash
     
    106108hpc-environment-sync.bash -m <modulename>/<module version>
    107109}}}
    108 To sync new resources use "-r" instead of "-m". To see the full list of options in the sync script use:
     110To see the full list of options in the sync script use:
    109111{{{
    110112hpc-environment-sync.bash -h
    111113}}}
    112114
    113 === running an already existing .eb file ===
    114  * eb YOURFILE.eb
    115  
    116115== FAQ ==
    117116=== error: The module file is already there ===