Changes between Version 1 and Version 2 of HPC_deploy


Ignore:
Timestamp:
2015-11-16T12:51:00+01:00 (9 years ago)
Author:
Roan Kanninga
Comment:

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  • HPC_deploy

    v1 v2  
    55If 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.
    66
    7 First an example of an custom !EasyBuild file created for deploying NGS_DNA on the cluster. Below the code there will be the explanation of all the steps in the script.
    8 
     7First 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.
     8{{{
    99name = 'NGS_DNA'
    1010version = '3.1.2'
    … …  
    3131
    3232moduleclass = 'bio'
     33}}}
     34'''name''' and '''version''' are pretty clear,
     35'''homepage''' and '''description'''; are recommended when releasing a future release of the tool.
     36'''toolchain'''; can be left like it is in the example (only when multiple tools need to be installed before this, you should use toolchain (see manual online of Easybuild).
     37'''easyblock'''; this is the type of data, tar.gz = ‘Tarball’ , executable = ‘Binary’ . All the different easyblocks are [https://github.com/hpcugent/easybuild-easyblocks/tree/master/easybuild/easyblocks/generic here]
     38If there any '''dependencies''' (in this case Molgenis-Compute), you put it in the name of your eb file (name will look like this: NGS_DNA-3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80)
     39'''Using variables''' instead of typing the same string 5 times is done with %s and then between () the name of the variable.
     40One necessary step is to set '''sanity_check_paths''', this is a check whether the file is unpacked/installed correctly.
     41All the installed eb configs are put automatically in the /apps/modules/all folder, but with '''moduleclass''' you can specify an extra module path.
     42N.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
    3343
    34 name and version are pretty clear,
    35 homepage and description; are recommended when releasing a future release of the tool.
    36 toolchain; can be left like it is in the example (only when multiple tools need to be installed before this, you should use toolchain (see manual online of Easybuild).
    37 easyblock; this is the type of data, tar.gz = ‘Tarball’ , executable = ‘Binary’ . All the different easyblocks are [https://github.com/hpcugent/easybuild-easyblocks/tree/master/easybuild/easyblocks/generic here]
    38 If there any dependencies (in this case Molgenis-Compute), you put it in the name of your eb file (name will look like this: NGS_DNA-3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80)
    39 Using variables instead of typing the same string 5 times is done with %s and then between () the name of the variable.
    40 One necessary step is to set sanity_check_paths, this is a check whether the file is unpacked/installed correctly.
    41 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
    42