Changes between Initial Version and Version 1 of HPC_deploy

Timestamp:

2015-11-16T12:48:48+01:00 (9 years ago)

Author:

Roan Kanninga

Comment:

--

HPC_deploy

@@ +1 @@
+Downloading and deploying tools is done with a tool called [https://hpcugent.github.io/easybuild/ EasyBuild]. This helps to get consistent installing and deploying of tools on the cluster.
+
+For most of the tools there is already an !EasyBuild file existing. These files are stored on github and are called easyconfigs and can be found [https://github.com/hpcugent/easybuild-easyconfigs/tree/master/easybuild/easyconfigs here]
+
+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.
+
+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.
+
+name = 'NGS_DNA'
+version = '3.1.2'
+namelower = name.lower()
+homepage = 'https://github.com/molgenis/molgenis-pipelines'
+description = """This distribution already contains several pipelines/protocols/parameter files which you can use 'out-of-the-box' to align and impute your NGS data using MOLGENIS Compute."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+easyblock = 'Tarball'
+
+#dependencies
+molname = 'Molgenis-Compute'
+molversion = 'v15.04.1-Java-1.7.0_80'
+versionsuffix = '-%s-%s' % (molname,molversion)
+dependencies = [(molname,molversion)]
+
+source_urls = [('http://github.com/molgenis/molgenis-pipelines/releases/download/%s/' % (version))]
+sources = [('%s-%s.tar.gz' % (name, version))]
+
+sanity_check_paths = {
+    'files': ['workflow.csv', 'parameters.csv'],
+    'dirs': []
+}
+
+moduleclass = 'bio'
+
+name and version are pretty clear, 
+homepage and description; are recommended when releasing a future release of the tool.
+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).
+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]
+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)
+Using variables instead of typing the same string 5 times is done with %s and then between () the name of the variable.
+One necessary step is to set sanity_check_paths, this is a check whether the file is unpacked/installed correctly. 
+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 
+