... | ... | @@ -17,7 +17,7 @@ You will need a unique context config file for each project. To get started go t |
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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 dependency fields 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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... | ... | @@ -92,7 +92,7 @@ A detailed description of each of the fields can be found below: |
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fusermount -u [cd]/[mount_work]*
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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. :so: Name this file to includes the project and the user
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Once you have filled out all of the fields click on the `| Save As |` button to save the file. :so: Name this file to includes the project and the user
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(:b: *contextconfig_local.txt* and *contextconfig_remote.txt* can be found in the *analysis/support/config* directory).
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Now when running a job you can simply load this file and it will populate the required fields for you. You can also use this text file as a template to quickly edit and create new context config files in a text editor.
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... | ... | @@ -103,7 +103,7 @@ There needs to be a unique batch config file created for each script in the pipe |
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![smallestcreatebatchconfig](/uploads/48f5df1610f2c60bbad7158a49b01dcd/smallestcreatebatchconfig.png)
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## Editing
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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 designated 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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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 designated 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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... | ... | @@ -120,7 +120,7 @@ This designates the job to be completed on the ____________server. |
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:b: The default depends on whether you loaded the local or remote file.
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**2. Replace String**
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* Replace strings is one of the most important aspects of batch_context. Replace string is the communication between the config, script and data files. You will need to create a string similar to the one below, initialising variables to be used in each of the loaded data files. Refer to [Creating Scripts](https://git.sharcnet.ca/jdesjard/batch_context/wikis/script-files) for more information. Notice that each varible is identified in **[]** brackets, then proceded by a **,** comma, and finally each variable is on a separate line.
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* Replace strings is one of the most important aspects of batch_context. Replace string is the communication between the config, script and data files. You will need to create a string similar to the one below, initialising variables to be used in each of the loaded data files. Refer to [Creating Scripts](https://git.sharcnet.ca/jdesjard/batch_context/wikis/script-files) for more information. Notice that each variable is identified in **[]** brackets, then proceded by a **,** comma, and finally each variable is on a separate line.
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:b: Script one: *scalpart.htb* looks for many variables in the swap string field, one of which is *[in_path]* which can be seen is initialised in the in the swap string field by: *[in_path],analysis/data/1_init*. By default these are already complete.
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![swapstringpopupgoodquality](/uploads/004e1ce8d684ed5c9315bc2ca34b3d41/swapstringpopupgoodquality.png)
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... | ... | @@ -182,7 +182,7 @@ These fields once filled out play a part in creating a *submit string* that is u |
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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. If you have multiple files open *Ctrl - Click* to select as many as you would like to save. These will **not** be combined into one 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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Once you have filled out all of the fields click on the `| Save As |` button to save. If you have multiple files open *Ctrl - Click* to select as many as you would like to save. These will **not** be combined into one 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_Script1.cfg* )
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Now when running a job you can simply load this file and it will populate the required fields for you. You can also use the text file created as a template to quickly edit and create new batch config files in a text editor.
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***
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