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Update Roddy as WorkflowManagementSystem authored by jpalbrecht's avatar jpalbrecht
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OTP-Documentation/Roddy-as-WorkflowManagementSystem.md
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...@@ -49,7 +49,7 @@ To update a Roddy Workflow the following steps have to be executed: ...@@ -49,7 +49,7 @@ To update a Roddy Workflow the following steps have to be executed:
1. Checkout the [otp-roddy-config](https://gitlab.com/one-touch-pipeline/otp-roddy-config) and update the configuration files 1. Checkout the [otp-roddy-config](https://gitlab.com/one-touch-pipeline/otp-roddy-config) and update the configuration files
- checkout git - checkout git
`git clone https://gitlab.com/one-touch-pipeline/otp-roddy-config` `git clone https://gitlab.com/one-touch-pipeline/otp-roddy-config` <br />
`git branch -b <RoddyWorkflow>_<1.1.1-1>` `git branch -b <RoddyWorkflow>_<1.1.1-1>`
- create the new template files (by copying old configuration files for example): - create the new template files (by copying old configuration files for example):
...@@ -58,24 +58,24 @@ resource-templates/lsf/<RoddyWorkflow>_<1.1.1-1>-wgs-queue.xml ...@@ -58,24 +58,24 @@ resource-templates/lsf/<RoddyWorkflow>_<1.1.1-1>-wgs-queue.xml
Don't forget to update the content of the files according to your needs! Don't forget to update the content of the files according to your needs!
- run the script `create-configs.sh` to autogenerate the configurations for each queue configured in `cluster-queue-names.txt` - run the script `create-configs.sh` to autogenerate the configurations for each queue configured in `cluster-queue-names.txt` <br />
This will create a lot configration files under `resource-generated/lsf/` with the naming schema `<RoddyWorkflow>_<1.1.1-1>-<SequencingMethod>-<qeueName>.xml` This will create a lot configration files under `resource-generated/lsf/` with the naming schema `<RoddyWorkflow>_<1.1.1-1>-<SequencingMethod>-<qeueName>.xml`
- push your changes to the new branch - push your changes to the new branch
`git commit -m "new configuration for <RoddyWorkflow>_<1.1.1-1>"` `git commit -m "new configuration for <RoddyWorkflow>_<1.1.1-1>"` <br />
`git push` `git push`
2. move to your roddy installation folder on the cluster and checkout the new branch. 2. move to your roddy installation folder on the cluster and checkout the new branch.
- connect to your cluster and prepare repository - connect to your cluster and prepare repository
`ssh yourUser@yourCluster.yourDomain.de` `ssh yourUser@yourCluster.yourDomain.de` <br />
`cd roddy/configs` `cd roddy/configs` <br />
`git checkout <RoddyWorkflow>_<1.1.1-1>` `git checkout <RoddyWorkflow>_<1.1.1-1>` <br />
- change directory to the roddy plugins folder and clone new <RoddyWorkflow> - change directory to the roddy plugins folder and clone new <RoddyWorkflow>
`cd roddy/plugins/<RoddyVersion>/` `cd roddy/plugins/<RoddyVersion>/` <br />
`bash ../../configs/scripts/checkout_roddy_plugin.sh <RoddyWorkflow> <1.1.1-1> `bash ../../configs/scripts/checkout_roddy_plugin.sh <RoddyWorkflow> <1.1.1-1>`
> >
> Roddy is in maintenance mode. No major releases will follow. > Roddy is in maintenance mode. No major releases will follow.
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