FragPipe

https://fragpipe.nesvilab.org/
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FragPipe is a comprehensive computational platform for mass spectrometry-based proteomics data...
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### Build FragPipe Installer (Windows)

Source: https://fragpipe.nesvilab.org/

Use this command to build the Windows installer. The output will be located in the FragPipe-GUI/build/installer directory.

```bash
cd FragPipe-GUI
./gradlew makeReleaseInstaller
```

--------------------------------

### Install X Window Packages on Ubuntu Server

Source: https://fragpipe.nesvilab.org/docs/tutorial_setup_x_forwarding.html

Installs necessary X window related packages on an Ubuntu server. Ensure your package lists are up-to-date before installation.

```bash
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install xorg openbox

```

--------------------------------

### Install MSstats Package

Source: https://fragpipe.nesvilab.org/docs/tutorial_msstats.html

Installs the MSstats package using BiocManager. Ensure BiocManager is installed first.

```R
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstats")

```

--------------------------------

### FragPipe Manifest File Format Example

Source: https://fragpipe.nesvilab.org/docs/tutorial_headless.html

Example of a tab-separated manifest file used to define LC-MS data files, experiment names, bioreplicates, and data types for FragPipe processing.

```plaintext
/storage/b1906_293T_proteinID_01A_QE3_122212.mzML	exp_a	1	DDA
/storage/b1922_293T_proteinID_02A_QE3_122212.mzML	exp_a	2	DDA
/storage/b1923_293T_proteinID_03A_QE3_122212.mzML	exp_b	1	DDA
/storage/b1924_293T_proteinID_04A_QE3_122212.mzML	exp_b	2	DDA
/storage/b1925_293T_proteinID_05A_QE3_122212.mzML	exp_c	1	DDA
```

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### Enter FragPipe Singularity Image

Source: https://fragpipe.nesvilab.org/docs/tutorial_docker.html

This command allows you to enter the Singularity image, binding a host directory to the container. Replace `/storage` with your desired host path if different.

```bash
singularity shell --compat --bind /storage:/storage fragpipe_latest.sif /bin/bash
```

--------------------------------

### TMT-16 Channel Annotation Example

Source: https://fragpipe.nesvilab.org/docs/tutorial_abpp.html

Example of TMT-16 channel annotations for a plex, mapping channel numbers to sample names. Ensure these match your experimental design.

```plaintext
126 DMSO-1
127N CL1-1
127C CL2-1
128N CL3-1
128C CL4-1
129N CL5-1
129C CL6-1
130N CL7-1
130C CL8-1
131N CL9-1
131C CL10-1
132N CL11-1
132C CL12-1
133N CL13-1
133C CL14-1
134N CL15-1
```

```plaintext
126 DMSO-2
127N CL1-2
127C CL2-2
128N CL3-2
128C CL4-2
129N CL5-2
129C CL6-2
130N CL7-2
130C CL8-2
131N CL9-2
131C CL10-2
132N CL11-2
132C CL12-2
133N CL13-2
133C CL14-2
134N CL15-2
```

--------------------------------

### Display FragPipe Help in Docker

Source: https://fragpipe.nesvilab.org/docs/tutorial_docker.html

After entering the Docker container, navigate to the FragPipe binary directory and execute this command to view available options and usage instructions.

```bash
./fragpipe --help
```

--------------------------------

### Run FragPipe Docker Container

Source: https://fragpipe.nesvilab.org/docs/tutorial_docker.html

Creates and enters a Docker container for FragPipe, mapping a host directory to a container directory. Replace `<host directory>` and `<container directory>` with your specific paths.

```bash
docker run -it -v <host directory>:<container directory> fcyucn/fragpipe /bin/bash
```

--------------------------------

### Pull FragPipe Singularity Image

Source: https://fragpipe.nesvilab.org/docs/tutorial_docker.html

Use this command to download the FragPipe Docker image for use with Singularity. Ensure Singularity is installed.

```bash
singularity pull docker://fcyucn/fragpipe:latest
```

--------------------------------

### Pull FragPipe Docker Image

Source: https://fragpipe.nesvilab.org/docs/tutorial_docker.html

Use this command to download the FragPipe Docker image from Docker Hub. Ensure Docker is installed on your system.

```bash
docker pull fcyucn/fragpipe
```

--------------------------------

### FragPipe Headless Mode Options

Source: https://fragpipe.nesvilab.org/docs/tutorial_headless.html

Available command-line options for FragPipe's headless mode, including help, workflow/manifest/workdir specification, dry run, memory/thread limits, and tool/binary path configurations.

```bash
Running without GUI. Usage:
        Windows: fragpipe.bat --headless --workflow <path to workflow file> --manifest <path to manifest file> --workdir <path to result directory>
        Linux: fragpipe --headless --workflow <path to workflow file> --manifest <path to manifest file> --workdir <path to result directory>
Options:
        -h
        --help                          # Print this help message.
        --headless                      # Running in headless mode.
        --workflow <string>             # Specify path to workflow file.
        --manifest <string>             # Specify path to manifest file.
        --workdir <string>              # Specify the result directory.
        --dry-run                       # (optional) Dry run, not really run FragPipe.
        --ram <integer>                 # (optional) Specify the maximum allowed memory size. The unit is GB. Set it to 0 to let FragPipe decide. Default = 0
        --threads <integer>             # (optional) Specify the number of threads. Default = core number - 1
        --config-tools-folder <string>  # (optional) specify the folder containing MSFragger, IonQuant, and dirTracer. If not specified, using the one in the cache.
        --config-diann <string>         # (optional) specify the location of the DIA-NN binary file (the actual executable file `DiaNN.exe`, not the DIA-NN installation file). If not specified, using the one in the cache. It could be from the previously configured or the build-in one.
        --config-python <string>        # (optional) specify the location of the Python directory. If not specified, using the one in the cache.
```

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### Connect to Remote Server with X Forwarding (Mac)

Source: https://fragpipe.nesvilab.org/docs/tutorial_setup_x_forwarding.html

Establishes an SSH connection to a remote server with X11 forwarding enabled. Replace 'username' and 'ip-address' with your actual credentials.

```bash
ssh -X username@ip-address

```
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