## Offload fastq data from the Ion Torrent at MGL
How to obtain fastq data from the Ion Torrent server at MGL. Requires that the plugin FileExporter has been run.

#### 1. Mount USB on system
Plug in the USB drive into the system.
Use `sudo fdisk -l` to find where your drive is mounted.
Mount via: `sudo mount /dev/sde1 /media/<your_drive>` (where /dev/sde1 is the location of drive found above, your_media is your drive name).

#### 2. Find the output files
If data is still on the system drive, the plugin results are here:
`/results/analysis/output/Home/<your_run>/plugin_out/FileExporter_XXX` (where XXX is a number of your FileExporter run)

If data has been archived, the plugin results are here:
`/mnt/nas-volumes-pool-share1/archivedReports/<your_run>/plugin_out/FileExporter_out.XXXX/`

#### 3. Compress the output files
Note: this will compress with gzip, but will delete the uncompressed files.
If the files are in the archive, just move them without compressing.
```
# Compress
gzip *.fastq
# Calculate md5
md5sum *.fastq.gz > <your_run.md5>
```

#### 4. Make output directory on the external drive and copy results
```
mkdir /media/<your_drive>/raw_data/<species>/<run_name> # Note: run_name is the same as your md5 name
# Move out of FileExporter folder
cd ..
rsync -avzP ./FileExporter_out.XXXX /media/<your_drive>/raw_data/<species>/<run_name>` # Note: XXXX is the FileExporter number
```

#### 5. Unmount
`sudo umount /media/<your_drive>`

#### 6. Move drive onto target computer
Use rsync as above to move the data onto your target computer, then make sure to check your md5 checksums:
`md5sum -c /<your>/<target>/<file>/<structure>/*.md5`

#### 7. Analyze away!