01. Clone repository and enter folder

git clone git clone https://github.com/sauloal/JBroseAutomaticInstanceCreator.git <INSTANCE NAME>
cd <INSTANCE NAME>

02. edit config

NAME=jbrowse_automatic_instance_creator
VER=1.12.1
IMG=jbrowse/gmod-jbrowse:${VER}

PORT=8006

NAME = Docker instance name - change if more than one instance to be run VER = JBrowse version (especifically, tag name of docker image) IMG = JBrowse Docker image name PORT = Port to run

03. create and edit data/<PROJECT_NAME>.cfg

REF=<REFERENCE FASTA NAME>
DB_NAME=<PROJECT_NAME>

04. remove or edit data/users.conf to disable/enable usernames and passwords access protection

USERS=(user1 user2 user3)
UPASS=(pass1 pass2 pass3)

05. create a project folder as defined in the .cfg file

mkdir data/<PROJECT_NAME>

06. inside the data/<PROJECT_NAME> folder create folders:

ref containing the fasta file as defined in data/<PROJECT_NAME>.cfg

e.g.: data/<PROJECT_NAME>/ref/<REFERENCE FASTA NAME>

bam containing bam and their index (.bam.bai) files (valid extensions: *.bam)

e.g.:

data/\<PROJECT_NAME\>/bam/data1.bam
data/\<PROJECT_NAME\>/bam/data1.bam.bai

gff containing GFF files (valid extensions: *.gff *.gff3 *.gff.gz *.gff3.gz)

e.g.:

data/\<PROJECT_NAME\>/gff/data1.gff

vcf VCF files and their index (.vcf.tbi or .vcf.gz.tbi) files (valid extensions: *.vcf *.vcf.gz)

e.g.:

data/\<PROJECT_NAME\>/vcf/data1.vcf
data/\<PROJECT_NAME\>/vcf/data1.vcf.tbi
data/\<PROJECT_NAME\>/vcf/data2.vcf.gz
data/\<PROJECT_NAME\>/vcf/data1.vcf.gz.tbi

NOTE: you can also create subfolders. they will appear as sub classes

e.g.:

gff/data1 - creating the category Annotation and track data1

gff/new/data1 - creating the category Annotation - new and track data1

gff/assembly/data1 - creating the category Annotation - assembly and track data1

07. optionally, create a .nfo file for each data file containing extra parameters for the track.

e.g.: for data1.vcf.gz create data1.vcf.gz.nfo

Available variables to be set are: LBL = Pretty name for track EXTRA = Extra parameters to be added to the configuration file GFF and Ref uses JSON BAM and VCF uses CONF file

Available variables to be used are: FILENAME = current track file name BN = basename of the current file DN = subfolder name of the current file CAT = category to be put under TYPE_DIR = file type folder (bam, vcf, gff, ref) CANVAS_TYPE = type of canvas to be plotted AS_JSON = whether the config is .json or .conf INDEX_EXT = extension of index file CLS = class KEY_EXT = key extension STORE_CLASS = store class CATEGORY = category name

JBROWSE       = JBrowse path
R_FOLDER      = project name
R_FOLDER_REF  = reference folder
R_FOLDER_BAM  = bam folder
R_FOLDER_GFF  = gff folder
R_FOLDER_VCF  = vcf folder
R_FOLDER_JSON = output json folder
R_JSON        = output json file
R_FASTA       = reference fasta file
TRACKS        = tracks.conf path
TRACKLIST     = trackList.json path
DATA_DIR      = path containing data
J_CONF        = global conf file path

GFFS          = GFF files found
VCFS          = VCF files found
BAMS          = BAM files found

e.g.:

LBL="Miraculous sample 1"
EXTRA="style.color = red"

08. The folder structure should look like this:

# base system files
<INSTANCE NAME>/config
<INSTANCE NAME>/edit.sh
<INSTANCE NAME>/fix_perm.sh
<INSTANCE NAME>/run.sh
<INSTANCE NAME>/LICENSE.md
<INSTANCE NAME>/README.md

# track scripts
<INSTANCE NAME>/data/config.sh
<INSTANCE NAME>/data/crypt.pl
<INSTANCE NAME>/data/gen_reg.scr
<INSTANCE NAME>/data/run.scr
<INSTANCE NAME>/data/secret.conf
<INSTANCE NAME>/data/users.conf

#project files
<INSTANCE NAME>/data/<PROJECT_NAME>.cfg
<INSTANCE NAME>/data/<PROJECT_NAME>/
<INSTANCE NAME>/data/<PROJECT_NAME>/ref/<REFERENCE>.fa
<INSTANCE NAME>/data/<PROJECT_NAME>/bam/
<INSTANCE NAME>/data/<PROJECT_NAME>/bam/data1.bam
<INSTANCE NAME>/data/<PROJECT_NAME>/bam/data1.bam.bai
<INSTANCE NAME>/data/<PROJECT_NAME>/bam/data1.bam.nfo
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/annotation/data1.gff
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/annotation/data1.gff.nfo
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/annotation/data1.gff3
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/annotation/data1.gff3.nfo
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/assembly/data1.gff
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/assembly/data1.gff.nfo
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/assembly/data1.gff3
<INSTANCE NAME>/data/<PROJECT_NAME>/gff/assembly/data1.gff3.nfo
<INSTANCE NAME>/data/<PROJECT_NAME>/vcf/
<INSTANCE NAME>/data/<PROJECT_NAME>/vcf/data1.vcf
<INSTANCE NAME>/data/<PROJECT_NAME>/vcf/data1.vcf.tbi
<INSTANCE NAME>/data/<PROJECT_NAME>/vcf/data1.vcf.nfo

09. run

./run.sh

This will:

• first time
  • index and convert the reference fasta
  • index and convert the gff file
• every time
  • symlink the indexed fasta data
  • symlink the indexed gff data
  • create .conf file for JBrowse with all the data found

10. open your browser at

http://<your ip address>:<port defined in config>

e.g.: http://127.0.0.1:8006