... | ... | @@ -9,14 +9,14 @@ This is a single config text file that specifies local and remote directories an |
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These are config text files are are unique to each pipeline *script*, but do not need to be changed according to the user or project. These handle the data file identification, pipeline order, software and computing resources of each of the scripts. It is recommended that these are named to mirror their corresponding scripts as they used hand in hand.
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(ie. *S1_Script1.htb* and *C1_Config_for_Script1.cfg* )
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If is highly suggested that you always save you config files in the support/config directory as text files. This will make them easy to edit and save outside of the batch_context user interface, as well as having an easy to load file when [Running the Scripts](https://git.sharcnet.ca/jdesjard/batch_context/wikis/running-scripts)
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If is highly suggested that you always save you config files in the support/config directory as text files. This will make them easy to edit and save outside of the batch_context user interface, as well as having an easy to load file when [Running Scripts](https://git.sharcnet.ca/jdesjard/batch_context/wikis/running-scripts).
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# Context configuration files (*.cfg)
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A user will need a unique context config file for each project. To get started go to:
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* *File -> Context Configuration*
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![smallestcreatecontextconfig](/uploads/d1632e0d4616b94e5235e3cca0821112/smallestcreatecontextconfig.png)
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## Editing
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You can create a new or edit and old context config in this user interface. To load an existing config file click on the |`Load Context Config`| button. You will need to fill out a number of fields depending on whether you will be running the job locally or remotely. All jobs must fill out the local dependancy feilds at the top of the block.
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You can create a new or edit and old context config in this user interface. To load an existing config file click on the |`Load Context Config`| button. You will need to fill out a number of fields depending on whether you will be running the job locally or remotely. All jobs must fill out the local dependency fields at the top of the block.
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![contextedit](/uploads/936947f6c07f2c7ba518432524a44d4d/contextedit.png)
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***
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A detailed description of each of the fields can be found below:
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![smallestcreatebatchconfig](/uploads/48f5df1610f2c60bbad7158a49b01dcd/smallestcreatebatchconfig.png)
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## Editing
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text
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You can create a new or edit and old batch config in this user interface. To load existing batch files click on the |`Get Batch Config File Names`| button. This interface allows you to look at and edit multiple config files at once. This helps you visualise the pipeline order, and ensure that every script you are using has a configuration file for it. You will need to fill out a number of fields depending on whether you will be running the job locally or remotely.
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![editconfigbuttons](/uploads/15cfea01e62161d13011548c19254ffe/editconfigbuttons.png)
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***
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text
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![sshsubmitline](/uploads/9775d9429b7326bf1c937e3a578eb121/sshsubmitline.png)
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***
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A detailed description of each of the fields can be found below:
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***
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**1. Execute Function**
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* Current Base
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text
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This signifies for the job to be completed locally.
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* Sq Sub
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text
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This signifies for the job to be completed on the ____________server.
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**2. Replace String**
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* text
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* text
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**8. Program Options**
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* text
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* text
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These fields once filled out play a part in creating a *submit string* that is used by the remote servers to correctly process the scripts. These strings are created for each data file for each scrip, and stored in the log folder.
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![sshsubmitline](/uploads/9775d9429b7326bf1c937e3a578eb121/sshsubmitline.png)
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***
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## Saving
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Once you have filled out all of the fields click on the |`Save As`| button to save the file. It is recommended that the files are named to mirror their corresponding scripts as they used hand in hand. (ie. *S1_Script1.htb* and *C1_Config_for_Script1.cfg* )
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