Difference: ProtocolsDcampCloning (1 vs. 3)

Cloning DCAMP for the first time:

1. cd $WORK
2. mkdir src
   1. Directory may already exist

1. cd src
2. git clone https://github.com/barricklab/dcamp.git

Updating to repository version of DCAMP

This assumes DCAMP has already been closed and will only work if this is true.

1. cd $WORK/src/DCAMP
2. git pull

This will update all files which have changed if there are any that need changing.

Pushing changes to DCAMP repository

This section assumes you have the permissions to push to DCAMP repository. If you don't and believe you should, speak to Jeff.

1. cd $WORK/src/DCAMP
2. git pull
   1. always make sure you are working with most recent version of DCAMP before trying to add new changes to avoid branching and conflicts
3. If adding new directories to DCAMP
   1. git add *
4. if adding new files to existing directories
   1. cd <Directory with new files>
   2. git add *
5. If adding specific files or directories
   1. git add <files>
   2. git add <path/to/add>
6. git commit -m "Your text here"
   1. This will put all files 'added' in the previous steps, and your commit message will be viewable on the web describing what changes you've made (examples include added new set of gd files related to X, or upated specific set of gd files with this information or for this reason)
7. git push
   1. Actually sends changes made back to DCAMP repository online for others to download.

Temporary DCAMP cloning instructions.

1. cd <location_of_choice
2. hg clone http://www.barricklab.org/hg/dcamp/
3. from here you should be able to navigate into the new dcamp/src/data directory and find the project folders containing .gd files for relevant samples
4. For Barrick lab members copying .gd files into a "01_Data" directory (likely on scratch) should allow gdtools download to directly download and expand relevant fastq files.