# Adding Library Files from Within a Project

Missing library files can be added when setting up tasks within a project, without having to navigate to the library file management page. The user interface will vary depending on the task and which library files already exist on your system. Below are two examples scenarios.

## Adding a missing whole genome aligner index (Bowtie 2 in this example)

1. Under the *Analyses* tab of a project, select an **Unaligned reads** data node
2. From the context sensitive menu on the right, choose **Aligners** followed by **Bowtie 2.** On the alignment task setup page, Partek Flow will display all assemblies that have a Bowtie 2 index (whole genome and transcriptome) in the *Assembly* drop-down list. If the assembly you want is missing, choose **New assembly…** from the drop-down list (Figure 1)

![Figure 1. The drop-down list will show all assemblies that have a Bowtie 2 index associated with them. Choose New assembly... to add a Bowtie 2 index to another assembly](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-129b3b81a6e47ddbbffa7a75f56f6b7924aa6268%2Fbowtie2-new-assembly.png?alt=media)

3. Choose the species and assembly in the *Add Bowtie 2 index* dialog. If the species and assembly you want do not appear in the drop-down lists, choose **New species...** and manually type the names (Figure 2)
4. Choose **Whole genome** from the *Index* drop-down list (Figure 2)
5. Select the **Build index** radio button (Figure 2)
6. Click **Create** (Figure 2)

![Figure 2. Add Bowtie 2 index to another assembly not listed in Figure 1.](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-79417504a297ab9f35ae31c1ceb5306a17799ce0%2Faligner-index-custom.png?alt=media)

Once the new Bowtie 2 index has been specified, you are able to queue the alignment task and it will execute once the Bowtie 2 index has been built.

## Add a missing gene set file for enrichment analysis

1. Under the *Analyses* tab of a project, select a **Feature list** data node
2. Choose **Biological interpretation** from the menu on the right, followed by **Gene set enrichment**
3. Select **Gene set database** radio button for *Database*. If the species and assembly you want do not appear in the *Assembly* drop-down list, select **New assembly...** (Figure 3)

![Figure 3. If no gene sets are associated with the assembly, click New assembly... to add one.](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-ce7c1c41f09bb5cf9fbfd9baa72fdf46a2d4935e%2FGO-new-assembly.png?alt=media)

4. If you are working with an assembly/species supported by Partek (e.g. human), choose a gene set from the *Gene set database* drop-down list (Figure 4), select the **Download gene set database** radio button and select **Create.** Alternatively, choose **Add gene set database** from the *Gene set database* drop-down list, manually type the custom gene set name and click **Create** to import your own gene set from the *Partek Flow server* or *URL* (Figure 5). Characters such as $ \* | \ : " < > ? / % cannot be used in custom names. If you are working with a custom species/assembly (e.g. for a non-model organism), only the *Add gene ontology source* option is available.

![Figure 4. Download a gene set database using the Create gene set database dialog from within a project](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-7e5c64fdf0a419b5f9a3b54f2e8eeb799abfe6a0%2Fcreate-gene-set-db.png?alt=media)

![Figure 5. Import a gene set database using the Create gene set database dialog from within a project](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d00c29ad7adbd340e4bf0dd89b8a24060a8a3c3c%2Fimport-gene-set-database.png?alt=media)

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.