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Fix spelling - apostrophe-s
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Ensembl's should not have it
users's should not have it
MathWork's to MathWorks's
else’s to else's (quote to apostrophe)
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Pär Lindfors committed Oct 18, 2024
1 parent 5566f4c commit 2478ae5
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2 changes: 1 addition & 1 deletion docs/cluster_guides/files.md
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Expand Up @@ -54,7 +54,7 @@ can read and execute your files and other people can not do anything.

Also note the `private` sub-folder: here you can put files that you want
only you, and no one else, to be able to access.
Each day we have a job that ensures that all users's private folders
Each day we have a job that ensures that all users private folders
still can't be accessed by anyone else,
even if the permissions somehow accidentally would change.

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2 changes: 1 addition & 1 deletion docs/databases/other_local.md
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Expand Up @@ -23,7 +23,7 @@ The dbCAN 4.0 database for automated carbohydrate-active enzyme annotation is no
The local path to the script for post-processing hmmscan --domtblout output is /sw/data/dbCAN/4.0/hmmscan-parser.sh. The CAZyDB trees have also been unpacked and are available in /sw/data/dbCAN/4.0/CAZyDB-phylogeny.
Variant Effect Predictor cache files

A local cache for all database files available for Ensembl's Variant Effect Predictor 87, 89 and 91 are available in directories /sw/data/vep/{87,89,91}. When module version vep/89 or vep/91 is loaded, the environment variable VEP_CACHE is set to the directory for the appropriate version. Local caches for versions 82, 84 and 86 exist only for homo_sapiens. To use the cached databases, run the script using the --cache option to indicate the use of a locally-cached database, and the --dir option to specify where this is:
A local cache for all database files available for Ensembl Variant Effect Predictor 87, 89 and 91 are available in directories /sw/data/vep/{87,89,91}. When module version vep/89 or vep/91 is loaded, the environment variable VEP_CACHE is set to the directory for the appropriate version. Local caches for versions 82, 84 and 86 exist only for homo_sapiens. To use the cached databases, run the script using the --cache option to indicate the use of a locally-cached database, and the --dir option to specify where this is:

vep --cache --dir $VEP_CACHE ...

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2 changes: 1 addition & 1 deletion docs/software/git_on_bianca.md
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Expand Up @@ -58,7 +58,7 @@ In the examples we use Rackham to mount the wharf directory. This is not the onl

### Cloning and pulling only

If you only want to run someone elses software that they have stored in a GitHub repo, you only need to clone the repo to be able to use it. Since you are only a user of the software there is no need to be able to push to the repo. If there are any updates to the repo you only need to pull the repo to get them.
If you only want to run someone else's software that they have stored in a GitHub repo, you only need to clone the repo to be able to use it. Since you are only a user of the software there is no need to be able to push to the repo. If there are any updates to the repo you only need to pull the repo to get them.

The way to do this on Bianca is to simply clone the repo on a computer with internet access, move it to the Bianca wharf, and then copy it to its final destination on Bianca. If there are any updates to the repo you want to get you move the repo back to the wharf, pull the updates to the mounted wharf directory on Rackham, then move the directory back to its final destination on Bianca.

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2 changes: 1 addition & 1 deletion docs/software/matlab.md
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Expand Up @@ -85,7 +85,7 @@ Using MATLAB on the cluster enables you to utilize high performance facilities l
- [Statistics and Machine Learning](https://se.mathworks.com/help/stats/index.html)
- [Deep Learning](https://se.mathworks.com/help/deeplearning/index.html)

[See MathWork's complete user guide](https://se.mathworks.com/help/parallel-computing/index.html?s_tid=CRUX_lftnav)
[See MathWorks's complete user guide](https://se.mathworks.com/help/parallel-computing/index.html?s_tid=CRUX_lftnav)

Some online tutorials and courses:

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