Changes between Version 22 and Version 23 of HPC_deploy

Timestamp:

2015-11-18T20:11:09+01:00 (9 years ago)

Author:

Pieter Neerincx

Comment:

--

HPC_deploy

@@ -11 +11 @@
 * Deployment of bioinformatics software is handled by the bioinformaticians from the ''depad'' group.
 
-If you want to become part of the ''depad'' group [wiki:Contact contact the helpdesk]. 
+If you want to join the ''depad'' group, please [wiki:Contact contact the helpdesk]. 
 The depad group uses [https://hpcugent.github.io/easybuild/ EasyBuild], which uses !EasyConfigs as recipes to enforce consistent, reproducible installations.
 In a nutshell an !EasyConfig deployment recipe can handle the following steps:
@@ -53 +53 @@
 * 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. 
 
-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.
+If there is no existing !EasyConfig, we have to create one ourselves.
 
-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.
+First 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.
 {{{
 name = 'NGS_DNA'
@@ -91 +91 @@
  * 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]]
 
-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
+For 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.
 
-=== installing a new tool ===
- * Create YOURFILE.eb file in /apps/sources/EasyBuild/custom/
+=== Installing the software ===
+ * Create a MyEasyConfig-1.2.3.eb file in {{{/apps/sources/EasyBuild/custom/}}}
  * module load !EasyBuild
- * eb YOURFILE.eb
+ * eb --robot --robot-paths=:/apps/sources/EasyBuild/custom/ /path/to/MyEasyConfig-1.2.3.eb
 
-Before you can execute the installed !EasyBuild file the module needs to be synced to the storage and nodes:
+=== Updating the Lmod caches and syncing installed software to nodes === 
+
+Before you can use the installed software it needs to be synced to various places and the Lmod caches needs to be updated:
 {{{ 
 sudo -u umcg-envsync bash 
@@ -106 +108 @@
 hpc-environment-sync.bash -m <modulename>/<module version>
 }}}
-To sync new resources use "-r" instead of "-m". To see the full list of options in the sync script use:
+To see the full list of options in the sync script use:
 {{{
 hpc-environment-sync.bash -h
 }}}
 
-=== running an already existing .eb file ===
- * eb YOURFILE.eb
- 
 == FAQ ==
 === error: The module file is already there ===