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Typo and link fixes
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asaravia-butler authored Oct 22, 2024
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- [Step 1: Install Singularity](#step-1-install-singularity)
- [Step 2: Fetch the Singularity Image](#step-2-fetch-the-singularity-image)
- [Step 3: Run the Workflow](#step-3-run-the-workflow)
- [Optional: Run the Annotations Database Creation Function as a Stand-Alone Script](#optional-run-the-annotations-database-creation-function-as-a-stand-alone-script)
- [Optional: Run the Annotations Database Creation Function as a Stand-Alone Script via Singularity](#optional-run-the-annotations-database-creation-function-as-a-stand-alone-script-via-singularity)
- [Approach 2: Using a Local R Environment](#approach-2-using-a-local-r-environment)
- [Step 1: Install R and Required R Packages](#step-1-install-r-and-required-r-packages)
- [Step 2: Run the Workflow](#step-2-run-the-workflow)
- [Optional: Run the Annotations Database Creation Function as a Stand-Alone Script](#optional-run-the-annotations-database-creation-function-as-a-stand-alone-script)
- [Optional: Run the Annotations Database Creation Function as a Stand-Alone Script via R](#optional-run-the-annotations-database-creation-function-as-a-stand-alone-script-via-r)

<br>

Expand Down Expand Up @@ -111,19 +111,21 @@ Rscript /work/GL-DPPD-7110-A_build-genome-annots-tab.R 'Mus musculus'

- No input files are required. Specify the species name of the target organism using a positional command line argument. `Mus musculus` is used in the example above.
> **Notes**:
> - To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
> - The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
> - To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
> - The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
- *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.


**Output data:**

- *-GL-annotations.tsv (Tab delineated table of gene annotations)

- *-GL-build-info.txt (Text file containing information used to create the annotation table, including tool and tool versions and date of creation)

<br>

#### *Optional*: Run the Annotations Database Creation Function as a Stand-Alone Script
#### *Optional*: Run the Annotations Database Creation Function as a Stand-Alone Script via Singularity

If the reference table does not specify an annotations database for the target organism in the 'annotations' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) file, the `install_annotations` function (defined in `install-org-db.R`) will be executed by default. This function can also be run as a stand-alone script:

Expand All @@ -139,7 +141,8 @@ Rscript /work/install-org-db.R 'Bacillus subtilis'
**Input data:**

- The species name of the target organism must be specified as the first positional command line argument. `Bacillus subtilis` is used in the example above.
> **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
> **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
- *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.


Expand Down Expand Up @@ -208,19 +211,21 @@ Rscript GL_RefAnnotTable-A_1.1.0/GL-DPPD-7110-A_build-genome-annots-tab.R 'Mus m

- No input files are required. Specify the species name of the target organism using a positional command line argument. `Mus musculus` is used in the example above.
> **Notes**:
> - To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
> - The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
> - To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
> - The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
- *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.


**Output data:**

- *-GL-annotations.tsv (Tab delineated table of gene annotations)

- *-GL-build-info.txt (Text file containing information used to create the annotation table, including tool and tool versions and date of creation)

<br>

#### *Optional*: Run the Annotations Database Creation Function as a Stand-Alone Script
#### *Optional*: Run the Annotations Database Creation Function as a Stand-Alone Script via R

If the reference table does not specify an annotations database for the target organism in the 'annotations' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) file, the `install_annotations` function (defined in `install-org-db.R`) will be executed by default. This function can also be run as a stand-alone script:

Expand All @@ -234,7 +239,8 @@ Rscript GL_RefAnnotTable-A_1.1.0/install-org-db.R 'Bacillus subtilis'
**Input data:**

- The species name of the target organism must be specified as the first positional command line argument. `Bacillus subtilis` is used in the example above.
> **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
> **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
- *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.


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