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GetStarted/create-a-new-project.md

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# Create a New Project
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1. Once the directories are set up and the necessary files are in place, run **genvisis.jar**.
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* Linux/Mac/Running remotely on Linux
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* Open a terminal and run **java -Xmx#g -jar [path]/genvisis.jar**
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* **#g** is the number of gigabytes of memory to use
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* [path] is the location of the genvisis.jar file
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* Example
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* **java -Xmx24g -jar ~/genvisis.jar** (if **genvisis.jar** is saved in your home directory)
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* Alternatively, locate **genvisis.jar** within a file manager and double-click on the Genvisis icon
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* Windows
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* Open a text file and write inside **java -Xmx#g -jar genvisis.jar**
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* **#g** is the number of gigabytes of memory to use
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* Example
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* **java -Xmx24g -jar genvisis.jar**
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* Save the text file as **vis.bat** in the same directory as **genvisis.jar**
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* Double-click **vis.bat**
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# Create a New Project in Genvisis
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![Image of Genvisis opened for the first time](/Images/GenvisisOpened.png)
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6. In the Genvisis window that opens, click **File****New Project**
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To create a new project, open Genvisis and then go to **File****New Project**.
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![Image of the Genvisis project creation window](/Images/NewProjectCreationWindow.png)
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7. Enter a **Project Name**
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8. Click **...** next to **Project Directory**
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9. Choose the **[ProjectDir]****Select**
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10. Click **...** next to **Source File Directory**
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11. Choose the **00src** directory created earlier → **Select**
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12. Genvisis will automatically detect the number of source files and the extension (eg. .csv, .csv.gz, .CEL, etc.).
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13. Choose the **Array Type** with which the data was collected:
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1. Enter a **Project Name**
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2. Click **...** next to **Project Directory**
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3. Choose the **[ProjectDir]****Select**
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4. Click **...** next to **Source File Directory**
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5. Choose the **00src** directory created earlier → **Select**
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6. Genvisis will automatically detect the number of source files and the extension (eg. .csv, .csv.gz, .CEL, etc.).
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7. Choose the **Array Type** with which the data was collected:
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* ILLUMINA
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* AFFY_GW6
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* Only SNP probesets
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* CEL files
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* APT results
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* Must have the same name as the **Project Name**
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14. **Genome Build** allows you to specify which version of the human genome to run the project in (e.g., **[Genome Reference Consortium Human Build 38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/)** (external link) aka **GRCh38**).
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8. **Genome Build** allows you to specify which version of the human genome to run the project in (e.g., **[Genome Reference Consortium Human Build 38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/)** (external link) aka **GRCh38**).
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* Unless there is a specific need to use an older version of the genome, set **Genome Build** to **HG38**, even if the manifest is in an older build. Genvisis can remap marker positions to **hg38** in the [Create Marker Positions](../#/documentation/RunTheGenvisisWorkflow--create-marker-positions-illumina) step of the Workflow.
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* To determine which version of the genome your data is in, check the **GenomeBuild** column of your Illumina manifest, or the header of your Affymetrix manifest.
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15. Select the locations for the following files:
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9. Select the locations for the following files:
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* **Illumina Manifest File** (if applicable)
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* **Pedigree File**
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* **Sample ID Linker File**
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* **Batch File**
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* **Marker Subset File**
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* Used only if you are not analyzing all markers in the manifest
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16. If using Illumina reports, **Create** will launch the **Validation Review** window. Fields will be automatically populated from the source files.
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10. If using Illumina reports, **Create** will launch the **Validation Review** window. Fields will be automatically populated from the source files.
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* Required
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* **Marker Name**
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* **Sample ID**
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![Image of the Validation Review window](/Images/ValidationReview.png)
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17. If the reports don’t have consistent headers, there will be a separate validation review window for each group of reports.
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18. Click **OK**.
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19. An audit will be performed to verify that the markers in the manifest are either 100% congruent with one of the reports, or that both the manifest and a report are 100% congruent with the Marker Subset File if one is provided.
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11. If the reports don’t have consistent headers, there will be a separate validation review window for each group of reports.
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12. Click **OK**.
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13. An audit will be performed to verify that the markers in the manifest are either 100% congruent with one of the reports, or that both the manifest and a report are 100% congruent with the Marker Subset File if one is provided.
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* If the manifest and the examined report match, a new project will be created and a new window will appear: **[Genvisis Project Workflow](../#/documentation/RunTheGenvisisWorkflow--introduction-to-the-workflow)**
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* If the manifest and examined report do not match, project creation will fail and you will need to create a Marker Subset File that lists only the markers shared between both files.
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20. If using Affymetrix CEL files, there will be no Validation Review and Genvisis will go directly to the **[Project Workflow](../#/documentation/RunTheGenvisisWorkflow--introduction-to-the-workflow)**.
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21. Several new files will be generated. Inside **[ProjectDir]** will be a file named **source_headers.ser** and the new sub-directory **logs/**. Inside **data/** will be the file **import.ser**.
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14. If using Affymetrix CEL files, there will be no Validation Review and Genvisis will go directly to the **[Project Workflow](../#/documentation/RunTheGenvisisWorkflow--introduction-to-the-workflow)**.
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15. Several new files will be generated. Inside **[ProjectDir]** will be a file named **source_headers.ser** and the new sub-directory **logs/**. Inside **data/** will be the file **import.ser**.

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