# Pipeline Library

# Pipeline Library

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">A pipeline is defined as a set of computational tools, which run either sequentially or parallelly to achieve a specific data analysis objective. Bioinformatics tools (and their respective commands) are designated as steps within a pipeline. Stanome provides a list of pre-configured pipelines evaluated against the model organisms in the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Pipeline Library</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #000000; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">.</span>

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Click the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"><span style="border-width: initial; border-style: none; display: inline-block; overflow: hidden; width: 53px; height: 25px;">![](https://lh3.googleusercontent.com/ozqTFSPmXxiUJuc3WVhLfWLRM9OGPOdnWMpgPtfoTm-m3cN-o7962MfnVDSBxWmMhjJw11nZ51hlYFZk5CMB7ZUI6xutRm6LzPQRif0WGLGiHWpHpEWnH_m0Tc6aKCDPe4TwCwzR)</span></span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> icon in the Utilities menu to access the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Pipeline Library</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> window (Fig. 1). The </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Pipeline Library</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> window shows the list view of all the pre-configured pipelines.</span>

![Fig. 1. The Pipeline Library window.](https://docs.stanome.com/uploads/images/gallery/2022-01/embedded-image-ulqccxeb.png)

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">The list view shows six fields:</span>

- - - <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Name:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> Pipeline name</span>
        - <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Execution Flow:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> Sequential order of the tools used in the pipeline</span>
        - <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Hub:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> Name of the relevant Hub</span>
        - <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Category:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> The functional tag(s) associated with the pipeline</span>
        - <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Description:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> Functional details of each tool</span>
        - <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">**Owner**: Owner of the pipeline</span>

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal;">Details of a pipeline can be viewed by clicking on the pipeline name. In addition to the list view, the pipeline window (Fig. 2) provides additional details about steps and tools. Go to pipeline creation to know more. Click the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal;"><span style="border-width: initial; border-style: none; display: inline-block; overflow: hidden; width: 20px; height: 20px;">![](https://lh4.googleusercontent.com/w3Jj_nUc-EDXAFwF1Qo_Hz4TsNxld9VBq_XXhGDggn559graCu9xIAu-iImXNVEvGMcQxRKNKx8-J0D6Z7_dwDP7_PVVSnA1VLxdFihTfq4tRKhcPN1rSLimpwMLB6eteEkBrgeK)</span></span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal;"> icon to go back to the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal;">Pipeline Library</span> <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal;">window. Users can’t delete pipelines from the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal;">Pipeline Library </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal;">but can copy them into individual projects and customize them according to their needs.</span></span>

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal;">![Fig. 2. A pipeline detail view.](https://docs.stanome.com/uploads/images/gallery/2022-01/embedded-image-hkid1qgi.png)</span></span>