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update mounting instructions #166

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13 changes: 9 additions & 4 deletions docs/cubic/cubic.md
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Expand Up @@ -304,6 +304,7 @@ It is also possible to copy files through the mount point, but this would be qui

## Method II: Mounting CUBIC in your local machine (interactive)


### Mounting CUBIC on your local machine using smb

One way to interact with CUBIC files is to _mount_ the server on to your filesystem. This can be useful for quickly moving a small number of files back and forth
Expand All @@ -330,19 +331,23 @@ cd
mkdir -p cbica/projects/<project_name>
chmod 700 cbica/projects/<project_name>
```
3. Using a text editor, create a file called `synthetic.conf` and save it in `/etc`. You will need to use `sudo` to make a file in `/etc`; e.g. `sudo vim /etc/synthetic.conf`.
4. Put the following text in the file. You must use a `tab` rather than space: `cbica /Users/my_home_folder/cbica`
5. Restart the computer.
6. You should now see a dir in the root dir, `/cbica`.

3. Mount the desired CUBIC directory to your newly created, local mount directory using SSHfs and CUBIC-sattertt
7. Mount the desired CUBIC directory to your newly created, local mount directory using SSHfs and CUBIC-sattertt
```bash
SSHfs -o defer_permissions <username>@CUBIC-login.uphs.upenn.edu:/cbica/projects/<project_name>/ /cbica/projects/<project_name>/
```
4. Unmount when done! You should run this unmount command from outside of the mount point.

8. Unmount when done! You should run this unmount command from outside of the mount point.
```bash
cd # just to make sure we are not inside the mount dir

umount /cbica/projects/<project_name> # note that command is not "unmount"!!
```

5. Make an alias for mounting project directory:
9. Make an alias for mounting project directory:
```bash
alias alias_name="SSHfs -o defer_permissions <username>@CUBIC-login.uphs.upenn.edu:/cbica/projects/<project_name> /cbica/projects/<project_name>/"
```
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