1. 1. 1. cd <location_for_repository>
      2. git clone https://github.com/barricklab/barricklab.git
      3. Do 1 of the following:
         • add <location_for_repository/barricklab> to your path (don't forget to put it in your profile)
         • run the command using the absolute path
         • move reads_to_gd_files.py to place within your path. This is the worst choice. NOTE: you will need to move the script each time you update from the repository

1. 1. 1. cd <location_for_repository/barricklab>
      2. git pull
      3. Remember to move reads_to_gd_files.py to somewhere in your path if you went with that option originally, and consider deleting it from that location and doing one of the other options.

• Be sure the first row contains the names you want included in the .gd files. (i.e. that the file has a header row)
• Be sure 'sample' is the first column
• Be sure file is tab separated

1. 1. cd <location_of_fastq_files>

• • • reads_to_gd_files.py -a <your_name> -f $PWD -r <location_of_references> -m <location_and_name_of_meta_data_tsv_file>
    • for <your_name> make sure you do not use spaces

• • • If there are index files in the directory (i.e. if your sequencing data comes from a miSeq run) add -i to the above command line
    • If the data is stored on TACC's corral system and is maintained by the Barrick lab, add -b to the above command line
    • If the data is stored on NCBI's SRA archive, add -s to the above command line

1. 1. Inspect contents of new_gd_files, and make sure both the files created and the contents of those files look correct.

• • • cd <location_of_dcamp>
    • hg pull
    • hg update
  1. If fastq files are part of a new project/publication, make a new RS_#### directory within DCAMP's src/data directory, otherwise determine what directory .gd files should belong to.
  2. cd <location_of_fastq_files>
  3. mv -i new_gd_files/*.gd <location_from_root_of_dcamp>/dcamp/src/data/<RS_####_directory>
  4. verify that the contents of new_gd_files are empty
     • ls new_gd_files
  5. rm -r new_gd_files
  6. cd <location_from_root_of_dcamp>/dcamp
  7. hg add .
  8. hg commit -m "<Brief description of what you are adding>"
  9. hg push

Version History.

• 3-30-16 GSAF Core seems to have changed the fastq file output naming system. No longer is the barcode added prior to the lane ID. Instead an unknown S# is added in front of it. S# varies per sample and does not appear to be related to the barcode. Script updated to account for new naming, but should retain old functionality as well

Genome Diff file Generation

Overview

This is a series of commands to automatically generate .gd files based on naming system present in .fastq files. This will typically be the first step once you have sequencing files in .fastq format from the sequencing core. Script exists as part of barricklab respository on github.

Protocol

Clone or update script from github repository:

• • Clone (for first time users):
    1. cd <location_for_repository>
    2. git clone https://github.com/barricklab/barricklab.git
    3. Do 1 of the following:
       • add <location_for_repository/barricklab> to your path (don't forget to put it in your profile)
       • run the command using the absolute path

• • update respository scripts (if you know there are changes or if something isn't working how you expect)
    1. cd <location_for_repository/barricklab>
    2. git pull

Generate meta data file

Generate .gd files

1. 1. cd <location_of_fastq_files>
   2. Run the following command and applicable options:
      • reads_to_gd_files.py -a <your_name> -f $PWD -r <location_of_references> -m <location_and_name_of_meta_data_tsv_file>

• • • If there are index files in the directory (i.e. if your sequencing data comes from a miSeq run) add -i to the above command line
    • If the data is stored on TACC's corral system and is maintained by the Barrick lab, add -b to the above command line
    • If the data is stored on NCBI's SRA archive, add -s to the above command line

Add .gd files to DCAMP

• • • cd <location_of_dcamp>

1. 1. If fastq files are part of a new project/publication, make a new RS_#### directory within DCAMP's src/data directory, otherwise determine what directory .gd files should belong to.
   2. cd <location_of_fastq_files>
   3. mv -i new_gd_files/*.gd <location_from_root_of_dcamp>/dcamp/src/data/<RS_####_directory>

1. 1. rm -r new_gd_files
   2. cd <location_from_root_of_dcamp>/dcamp

Version History.

-- Main.DanielDeatherage - 29 Mar 2016

Genome Diff file Generation

Overview

This is a series of commands to automatically generate .gd files based on naming system present in .fastq files. This will typically be the first step once you have sequencing files in .fastq format from the sequencing core. Script exists as part of barricklab respository on github.

Protocol

Version History.

-- Main.DanielDeatherage - 29 Mar 2016

Genome Diff file Generation

Overview

This is a series of commands to automatically generate .gd files based on naming system present in .fastq files. This will typically be the first step once you have sequencing files in .fastq format from the sequencing core. Script exists as part of barricklab respository on github.

Protocol

1. Clone or update script from github repository:
   • Clone for first time users:
     1. cd <location_within_path>
     2. =git clone https://github.com/barricklab/barricklab.git =

Version History.

-- Main.DanielDeatherage - 29 Mar 2016