...
| Table of Contents |
|---|
Introduction
UCSC genome bioinformatics supports mammalian, insect, fish, avian, and some fungal genomes.
IGBQuickLoad contains genome directories with sequence and annotations data for some (not all) genome assemblies supported at UCSC.
The following describes how to add a new genome version to the IGB QuickLoad repository and update IGB species.txt.
Command-line utilities you'll need need
- faToTwoBit from UCSC (needed if there is no 2Bit file available)
- twoBitInfo from UCSC (needed to generate the genome.txt file)
- UNIX wget (not installed by default on Mac but available on most other UNIX systems)
- UNIX sort (should be pre-installed on any UNIX system, including Mac)
- IGBQuickLoad scripts in genomes/pub/src subversion repo.
Compiled UCSC software tools are available from http://hgdownload.cse.ucsc.edu/admin/exe/
...
.
...
Get
...
the
...
compiled
...
programs
...
these
...
in
...
a
...
directory
...
in
...
your
...
PATH.
...
Make
...
sure
...
they
...
are
...
executable
...
on
...
your
...
system.
...
If
...
you're
...
doing
...
this
...
on
...
a
...
Mac
...
desktop
...
or
...
laptop
...
computer,
...
create
...
a
...
directory
...
called
...
"bin"
...
in
...
your
...
home
...
directory
...
and
...
save
...
all
...
compiled
...
binaries
...
there.
...
Edit
...
your
...
.bash_profile
...
file
...
to
...
include
...
a
...
line
...
like
...
the
...
following
...
to
...
ensure
...
that
...
the
...
shell
...
can
...
find
...
the
...
programs.
...
| Code Block |
|---|
export PATH=.:$HOME/bin:$PATH
{code}
|
For
...
example,
...
the
...
following
...
sequence
...
of
...
commands
...
downloads
...
the
...
software,
...
moves
...
it
...
to
...
a
...
directory
...
named
...
"bin"
...
in
...
the
...
home
...
directory,
...
and
...
then
...
makes
...
it
...
executable
...
using
...
the
...
chmod
...
command.
...
| Code Block |
|---|
wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/twoBitInfo
mv twoBitInfo ~/bin
chmod a+x ~/bin/twoBitInfo
{code}
h1. |
Step-by-step
...
guide
...
to
...
adding
...
a
...
new
...
UCSC
...
genome
...
to
...
IGBQuickLoad
...
The
...
following
...
instructions
...
explain
...
how
...
to
...
- set
...
- up
...
- your
...
- local
...
- copy
...
- of
...
- the
...
- public
...
- QuickLoad
...
- data
...
- repository
- set up your environment to run QuickLoad scripts
- get annotation files and sequence files from UCSC Genome Bioinformatics
- convert files to random access, indexed file formats that enable partial data loading in IGB
- update meta-data files IGB requires to update its interface and allow users to access the newly added genome
- update HEADER.html and other files describing the new genome
- commit your new files and updates the repo
- submit a Jira ticket requesting that the main site and mirror sites be updated
If you have questions don't hesitate to ask Ann.
Get the QuickLoad data repo
Check out or update a copy of IGB QuickLoad data directories.
Open a terminal (UNIX shell) and change into the directory where you want your checked-out copy of the genomes repository to reside.
For example, you might do this:
| Code Block |
|---|
cd # change into your home directory
svn co https://svn.transvar.org/repos/genomes/trunk/pub/quickload
{code}
|
Or,
...
if
...
you
...
already
...
have
...
a
...
copy,
...
just
...
update
...
using
...
svn
...
up.
...
| Code Block |
|---|
svn up
{code}
|
This
...
will
...
update
...
everything
...
in
...
the
...
current
...
working
...
directory
...
and
...
all
...
the
...
directories
...
beneath
...
it.
...
To
...
avoid
...
conflicts
...
with
...
other
...
people's
...
committed
...
changes,
...
be
...
sure
...
to
...
update
...
your
...
local
...
copy
...
of
...
IGB
...
QuickLoad
...
repo
...
before
...
starting
...
work.
...
Questions
...
about
...
using
...
subversion?
...
See:
...
...
...
...
...
.
Configure your Apache web server to server the IGB QuickLoad data directories via http
You'll need this to test that the new genome directory looks OK when visited in a Web browser. How you do this will depend on your computer. The following instructions explain how to do this on a Mac.
- Use
locateto find your local copy ofhttpd.conf, the Apache configuration file. Probably it's located at/private/etc/apache2/httpd.conf
...
- ,
...
- depending
...
- on
...
- your
...
- system.
...
- Open
...
- a
...
- terminal
...
- window
...
- and
...
- change
...
- into
...
- the
...
- same
...
- directory
...
- as
...
- the
...
- configuration
...
- file.
...
- Make
...
- a
...
- backup
...
- copy
...
- of
...
- the
...
- file:
...
| Code Block |
|---|
cp httpd.conf httpd.conf.bak
{code}
* Use sudo to open the file in a text editor like {{pico}} or {{emacs}} and enter your password. \*Note\* this only works if you have admin privileges on your computer. If you can't edit this file, then you'll need to get help before proceeding.
{code} |
- Use sudo to open the file in a text editor like
picooremacsand enter your password. *Note* this only works if you have admin privileges on your computer. If you can't edit this file, then you'll need to get help before proceeding.
| Code Block |
|---|
sudo pico httpd.conf
{code}
* Find the place in the file that says *DocumentRoot*. Comment the current DocumentRoot and substitute the full path to your checked-out copy of the QuickLoad repository:
{code} |
- Find the place in the file that says DocumentRoot. Comment the current DocumentRoot and substitute the full path to your checked-out copy of the QuickLoad repository:
| Code Block |
|---|
#DocumentRoot "/Library/WebServer/Documents"
DocumentRoot "/Users/username/quickload"
{code}
and
{code} |
and
| Code Block |
|---|
#<Directory "/Library/WebServer/Documents">
<Directory "/Users/username/quickload">
{code}
where {{quickload}} is your copy of the |
where quickload is your copy of the checked-out
...
repo.
...
- Restart
...
- Apache.
...
- To
...
- restart
...
- Apache
...
- on
...
- a
...
- Mac,
...
- open
...
- Apple
...
- >
...
- System
...
- Preferences
...
- ...
...
- >
...
- Sharing
...
- and
...
- select
...
- Web
...
- Sharing
...
- .
...
- If
...
- it
...
- is
...
- already
...
- selected,
...
- that
...
- means
...
- Apache
...
- is
...
- already
...
- running.
...
- Unselect
...
- it
...
- to
...
- stop
...
- Apache
...
- and
...
- then
...
- select
...
- it
...
- again
...
- to
...
- restart
...
- Apache.
...
- Open
...
- a
...
- Web
...
- browser
...
- and
...
- enter
...
- url
...
...
- .
...
- (You
...
- may
...
- need
...
- to
...
- refresh
...
- your
...
- browser.)
...
- You
...
- should
...
- see
...
- now
...
- see
...
- something
...
- that
...
- looks
...
- exactly
...
- like
...
- the
...
- public
...
- IGB
...
- QuickLoad
...
- site.
...
| Note |
|---|
Now, you can configure IGB to access your local copy of IGB QuickLoad using both the URL [] \* *or* \*using the file chooser because IGB supports QuickLoad access via
Web (http) or from local files. {note} h3. Check out or update a copy of IGB QuickLoad source code |
Check out or update a copy of IGB QuickLoad source code (src)
...
directory.
...
As
...
before,
...
open
...
a
...
terminal
...
and
...
change
...
into
...
the
...
directory
...
where
...
you
...
want
...
your
...
checked-out
...
copy
...
of
...
the
...
genomes
...
src
...
code
...
to
...
reside.
...
A
...
good
...
place
...
for
...
checked-out
...
code
...
is
...
a
...
directory
...
named
...
src
...
in
...
your
...
home
...
directory.
...
To
...
set
...
up
...
a
...
src
...
directory
...
for
...
checked-out
...
code:
...
| Code Block |
|---|
cd
mkdir src
cd src
{code}
|
Then,
...
use
...
svn
...
to
...
get
...
a
...
copy
...
of
...
the
...
QuickLoad
...
source
...
code
...
from
...
the
...
repo
...
and
...
save
...
it
...
to
...
a
...
directory
...
named
...
quickload_src:
...
| Code Block |
|---|
$ svn co https://svn.transvar.org/repos/genomes/trunk/pub/src quickload_src
{code}
|
To
...
ensure
...
that
...
you'll
...
be
...
able
...
to
...
run
...
the
...
code,
...
add
...
the
...
new
...
directory
...
to
...
your
...
PATH
...
and
...
your
...
PYTHONPATH
...
environmental
...
variables
...
by
...
editing
...
your
...
.bash_profile
...
startup
...
script:
...
| Code Block |
|---|
export PATH=$HOME/src/quickload_src:$PATH
export PYTHONPATH=$HOME/src/quickload_src:$PYTHONPATH
{code}
*Test that it worked* by opening a new terminal and typing {{sample.py}} at the prompt. If your path is correctly configured, the script will run without error.
h2. Get the data from UCSC
h3. Open a Web browser and find the genome you would like to add in the Table Browser at UCSC
Go to [ |
Test that it worked by opening a new terminal and typing sample.py at the prompt. If your path is correctly configured, the script will run without error.
Get the data from UCSC
Open a Web browser and find the genome you would like to add in the Table Browser at UCSC
Go to http://genome.ucsc.edu/cgi-bin/hgTables
...
Use the genome version menu to determine the month and year of the genome release you want.
Make note of the genome version synonyms UCSC is using. This usually in parentheses next to the month and year of the release. These will need to be included in IGB's curated list of genome version synonyms to ensure compatibility with Galaxy, UCSC DAS, or other external resources.
For example, the assembly menu for zebrafish reads Jul. 2010 (Zv9/danRer7).
...
The
...
terms
...
in
...
parentheses
...
are
...
genome
...
version
...
synonyms
...
for
...
this
...
assembly.
...
The
...
one
...
on
...
the
...
right
...
(danRer7)
...
is
...
what
...
UCSC
...
calls
...
the
...
"database"
...
for
...
this
...
assembly
...
and
...
is
...
used
...
as
...
identifier
...
of
...
the
...
genome
...
in
...
the
...
UCSC
...
DAS1
...
data
...
source.
...
The
...
term
...
on
...
left
...
(Zv9)
...
is
...
usually
...
another
...
commonly-used
...
term,
...
sometimes
...
assigned
...
by
...
the
...
sequencing
...
consortium
...
that
...
generated
...
the
...
assembly
...
or
...
the
...
original
...
sequence.
...
Sometimes,
...
however,
...
this
...
term
...
is
...
not
...
unique.
...
For
...
example,
...
some
...
genome
...
versions
...
are
...
reported
...
with
...
the
...
term
...
"Broad,"
...
which
...
is
...
an
...
organization,
...
not
...
an
...
assembly.
...
Name
...
the
...
genome
...
for
...
genus,
...
species,
...
strain
...
(optional),
...
release
...
month
...
and
...
year
...
Choose
...
an
...
IGB
...
genome
...
assembly
...
version
...
identifier
...
to
...
represent
...
the
...
UCSC
...
genome.
...
IGB
...
genome
...
assembly
...
versions
...
identifiers
...
look
...
like:
...
IGB
...
uses
...
genus,
...
species,
...
strain
...
(optionally),
...
and
...
release
...
month
...
and
...
year
...
to
...
identify
...
genome
...
assembly
...
versions
...
for
...
a
...
species,
...
individual,
...
strain,
...
or
...
cultivar
...
whose
...
genome
...
was
...
sequenced.
...
G_species_strain_Mmm_
...
YYYY
where
- G is the first letter (upper-case)
...
- of
...
- the
...
- genus
...
- name
...
- species
...
- is
...
- the
...
- species
...
- name
...
- (lower-case)
...
- strain
...
- is
...
- cultivar,
...
- strain,
...
- or
...
- individual
...
- whose
...
- genome
...
- was
...
- sequenced
...
- (this
...
- is
...
- optional
...
- and
...
- not
...
- usually
...
- needed
...
- for
...
- UCSC-managed
...
- genomes)
...
- Mmm
...
- is
...
- the
...
- three-letter
...
- English
...
- abbreviation
...
- of
...
- the
...
- month
...
- of
...
- the
...
- release
...
- (first
...
- letter
...
- is
...
- upper-case)
...
- YYYY
...
- is
...
- the
...
- year
...
- of
...
- the
...
- release
...
Examples)
...
- P_troglodytes_Oct_2010
...
- genome
...
- assembly
...
- for
...
- chimp
...
- released
...
- Oct
...
- 2010
...
- Z_mays_B73_Mar_2010
...
- genome
...
- assembly
...
- for
...
- maize
...
- plant
...
- cultivar
...
- B73
...
- released
...
- March
...
- 2010
...
Use
...
svn
...
mkdir
...
to
...
create
...
a
...
new
...
genome
...
version
...
directory
...
for
...
the
...
genomes
...
repo
...
Use
...
svn
...
mkdir
...
to
...
create
...
a
...
new
...
genome
...
directory.
...
The
...
name
...
of
...
the
...
new
...
directory
...
should
...
be
...
identical
...
to
...
the
...
IGB
...
QuickLoad
...
genome
...
version
...
name.
...
| Code Block |
|---|
svn mkdir G_species_Mmm_YYYYY
{code}
{warning}
|
| Warning |
|---|
Don't use the UNIX mkdir command to create the directory and then use svn add later to add it later to the repo. If you do this and are not careful, you will accidentally add large sequence data files to the repo. {warning} Change directories into the newly created genome version directory {code} |
Change directories into the newly created genome version directory
| Code Block |
|---|
cd G_species_Mmm_YYYYY
{code}
h3. Download the sequence data
Go to UCSC Genome Bioinformatics and click Downloads > Genome Data. Click the link for your species and then click the link labeled Full data set.
This will take you to a directory where you can download files. Typically, the address of the directory is
[ |
Download the sequence data
Go to UCSC Genome Bioinformatics and click Downloads > Genome Data. Click the link for your species and then click the link labeled Full data set.
This will take you to a directory where you can download files. Typically, the address of the directory is
http://hgdownload.soe.ucsc.edu/goldenPath/UCSCNAME
...
For example,
...
UCSC's
...
danRer7
...
genome
...
is
...
in
...
http://hgdownload.soe.ucsc.edu/goldenPath/danRer7/bigZips/
...
.
...
Is
...
the
...
2bit
...
file
...
available?
...
For
...
most
...
of
...
the
...
more
...
recent
...
genomes,
...
UCSC
...
is
...
using
...
the
...
2bit
...
format
...
to
...
distribute
...
sequence
...
data.
...
However,
...
some
...
older
...
versions
...
may
...
not
...
make
...
this
...
available.
...
If
...
yes,
...
download
...
it
...
using
...
wget.
...
Right-click
...
the
...
link
...
in
...
your
...
browser
...
and
...
select
...
"Copy
...
Link
...
Location."
...
Return
...
to
...
your
...
terminal
...
UNIX
...
shell,
...
type
...
wget,
...
and
...
paste
...
the
...
URL
...
into
...
the
...
shell.
...
For
...
example,
...
| Code Block |
|---|
wget http://hgdownload.soe.ucsc.edu/goldenPath/danRer7/bigZips/danRer7.2bit
{code}
h6. Rename the file to |
Rename the file to G_species_Mmm_YYYYY.2bit.
...
The
...
prefix
...
(file
...
name
...
part)
...
of
...
the
...
2bit
...
file
...
for
...
a
...
genome
...
should
...
be
...
the
...
genome
...
version
...
identifier
...
and
...
suffix
...
(file
...
extension)
...
should
...
be
...
2bit.
...
For
...
example,
...
| Code Block |
|---|
mv danRer7.2bit D_rerio_Jul_2010.2bit {code} h5. If |
If not,
...
download
...
the
...
sequence
...
data
...
in
...
fasta
...
format.
...
For
...
older
...
genomes,
...
UCSC
...
provides
...
sequence
...
data
...
in
...
a
...
so-called
...
"bigZip"
...
file
...
which
...
contains
...
each
...
assembled
...
sequence
...
(typically
...
one
...
per
...
physical
...
chromosome)
...
in
...
a
...
separate
...
fasta
...
file.
...
For
...
example,
...
as
...
of
...
this
...
writing,
...
the
...
dm3
...
(fruit
...
fly)
...
genome
...
is
...
provided
...
in
...
this
...
format.
...
Right-click
...
the
...
link
...
in
...
your
...
browser
...
and
...
select
...
"Copy
...
Link
...
Location."
...
Return
...
to
...
your
...
terminal
...
UNIX
...
shell,
...
type
...
wget,
...
and
...
paste
...
the
...
URL
...
into
...
the
...
shell.
...
For
...
example,
...
| Code Block |
|---|
wget http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/chromFa.tar.gz
{code}
h6. Unpack the file
Use tar with options xvf to uncompress the file while also extracting its contents. An |
...
Unpack the file
...
Use tar with options xvf to uncompress the file while also extracting its contents. An ".fa"
...
file
...
for
...
each
...
chromosome
...
will
...
appear
...
when
...
completed.
...
| Code Block |
|---|
tar xvf chromFa.tar.gz
{code}
{note}
Once |
| Note |
|---|
Once you've created the 2bit file for the genome assembly, you'll delete the .fa and the .gz files. {note} h6. Create 2bit file using faToTwoBit Get faToTwoBit installed. In the following example, the MacOS version is downloaded: {code} |
...
Create 2bit file using faToTwoBit
...
Get faToTwoBit installed. In the following example, the MacOS version is downloaded:
| Code Block |
|---|
wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/faToTwoBit
mv faToTwoBit ~/bin
chmod a+x ~/bin/faToTwoBit
{code}
|
h7.
...
Convert
...
the
...
fa
...
files
...
to
...
twoBit
...
faToTwoBit
...
will
...
read
...
one
...
or
...
more
...
fasta
...
files
...
and
...
convert
...
them
...
to
...
a
...
single
...
2bit
...
file.
...
To
...
understand
...
how
...
to
...
run
...
it,
...
type
...
the
...
name
...
of
...
the
...
program.
...
If
...
you
...
run
...
it
...
without
...
any
...
arguments,
...
it
...
will
...
...
a
...
usage
...
message.
...
| Code Block |
|---|
faToTwoBit
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
options:
-noMask - Ignore lower-case masking in fa file.
-stripVersion - Strip off version number after . for genbank accessions.
-ignoreDups - only convert first sequence if there are duplicates
{code}
|
The
...
prefix
...
(file
...
name
...
part)
...
of
...
the
...
2bit
...
file
...
you
...
create
...
for
...
this
...
genome
...
version
...
should
...
be
...
the
...
genome
...
version
...
identifier
...
and
...
suffix
...
(file
...
extension)
...
should
...
be
...
"2bit."
...
| Code Block |
|---|
faToTwoBit *.fa G_species_Mmm_YYYY.2bit
{code}
h6. Delete |
Delete .fa
...
files
...
and
...
the
...
chromFa.tar.gz
...
file
| Code Block |
|---|
rm *.fa
rm chromFa.tar.gz
{code}
{note}
You can always |
| Note |
|---|
You can always re-create the .fa files using twoBitToFa, another UCSC tool. {note} {note} The 2bit file is typically smaller than the compressed |
| Note |
|---|
The 2bit file is typically smaller than the compressed chromFa.tar.gz file it replaced. Unlike the .tar.gz file, it supports random access, allowing IGB to support partial loading of sequence from the IGBQuickLoad site into the coordinates track. {note} h3. Makecoordinates track. |
Make genome.txt
...
file
...
Use
...
twoBitInfo
...
to
...
create
...
a
...
genome.txt
...
file
...
for
...
the
...
genome.
...
This
...
file
...
lists
...
sequences
...
and
...
their
...
sizes
...
for
...
the
...
genome.
...
| Code Block |
|---|
twoBitInfo G_species_Mmm_YYYY.2bit genome.txt
{code}
{note}
You can use twoBitInfo to make BED files marking the location of N's in the genome or calculate the amount of non-N sequence in an assembly.
{note}
h4. Sort the genome.txt file sequence size
The order of sequences listed in the genome.txt is how they will appear in the IGB Current Sequence tab when users visit the genome version in IGB.
Check the genome.txt file. Are the chromosomes listed in a reasonable order?
If you created the 2bit file from fasta files, then probably they will be listed in alphabetical.
Depending on the state of the genome assembly, i.e., how close to complete it is, it's usually much better to list the chromosomes by size, with larger sequences appearing first in the list.
To ensure that the chromosomes are listed with largest ones first, sort the file
{code} |
| Note |
|---|
You can use twoBitInfo to make BED files marking the location of N's in the genome or calculate the amount of non-N sequence in an assembly. |
Sort the genome.txt file sequence size
The order of sequences listed in the genome.txt is how they will appear in the IGB Current Sequence tab when users visit the genome version in IGB.
Check the genome.txt file. Are the chromosomes listed in a reasonable order?
If you created the 2bit file from fasta files, then probably they will be listed in alphabetical.
Depending on the state of the genome assembly, i.e., how close to complete it is, it's usually much better to list the chromosomes by size, with larger sequences appearing first in the list.
To ensure that the chromosomes are listed with largest ones first, sort the file
| Code Block |
|---|
sort -k2,2nr genome.txt > tmp
mv tmp genome.txt
{code}
h4. Add |
Add genome.txt
...
to
...
the
...
repo
...
Add
...
the
...
genome.txt
...
file
...
to
...
the
...
repo
...
| Code Block |
|---|
svn add genome.txt
{code}
h2. Edit |
Edit contents.txt
...
Add
...
the
...
new
...
genome
...
to
...
the
...
contents.txt
...
in
...
the
...
top
...
level
...
of
...
your
...
checked-out
...
quickload
...
directory.
...
The
...
contents.txt
...
file
...
is
...
a
...
tab-separated
...
file
...
with
...
two
...
columns:
...
- Column
...
- 1
...
- -
...
- genome
...
- directory
...
- Column
...
- 2
...
- -
...
- genome
...
- title
...
The
...
genome
...
title
...
is
...
what
...
IGB
...
will
...
display
...
in
...
the
...
title
...
bar
...
when
...
users
...
visit
...
the
...
new
...
genome.
...
To
...
create
...
the
...
title,
...
follow
...
the
...
same
...
conventions
...
as
...
for
...
the
...
other
...
UCSC
...
genomes.
...
Title
...
begins
...
with
...
genus
...
and
...
species,
...
followed
...
by
...
the
...
date
...
of
...
the
...
release
...
(in
...
parentheses),
...
followed
...
by
...
the
...
common
...
name
...
for
...
the
...
species,
...
followed
...
by
...
the
...
UCSC
...
genome
...
name
...
(in
...
parentheses).
...
For
...
example,
...
| Code Block |
|---|
Cavia porcellus (Feb 2008) guinea pig (cavPor3)
{code}
{warning}
Note that this file is |
| Warning |
|---|
Note that this file is tab-separated, so when you edit the file, be sure to use a tab character to separate the genome version and geome title fields. {warning} h1. Edit files to make the Web site look nicer. The main job of a QuickLoad site is to enable users to load data into IGB. However, a QuickLoad site is also a Web site, and so it's important to provide some additional files for users who visit the site in their Web browser. When you add a new set of files to the main IGBQuickLoad site, you need to also: * provide appropriate HEADER.html files for the genome version directory * edit the .htacess file in the QuickLoad root directory (one level above the genome version directories) h2. Add a new HEADER.html file to the genome directory. For this, use the script named {{writeQuickLoadHeaderUCSC.py}}. To run it, make sure you are in the top level of the QuickLoad directory and enter: {src} |
Edit files to make the Web site look nicer.
The main job of a QuickLoad site is to enable users to load data into IGB. However, a QuickLoad site is also a Web site, and so it's important to provide some additional files for users who visit the site in their Web browser. When you add a new set of files to the main IGBQuickLoad site, you need to also:
- provide appropriate HEADER.html files for the genome version directory
- edit the .htacess file in the QuickLoad root directory (one level above the genome version directories)
Add a new HEADER.html file to the genome directory.
For this, use the script named writeQuickLoadHeaderUCSC.py. To run it, make sure you are in the top level of the QuickLoad directory and enter:
| Code Block |
|---|
writeQuickLoadHeaderUCSC.py G_species_MMMMmm_YYYY > G_species_MMMMmm_YYYY/HEADER.html {src} |
The
...
script
...
will
...
read
...
the
...
contents.txt
...
file,
...
look
...
for
...
the
...
human-readable
...
title
...
of
...
the
...
genome
...
(column
...
2)
...
for
...
the
...
directory
...
G_species_
...
Mmm_YYYY,
...
and
...
then
...
...
text
...
for
...
HEADER.html
...
to
...
stdout.
...
Edit the .htaccess
...
file
...
When
...
users
...
open
...
a
...
location
...
in
...
the
...
IGB
...
QuickLoad
...
site
...
using
...
their
...
Web
...
browser,
...
the
...
browser
...
displays
...
a
...
list
...
of
...
files
...
and
...
some
...
descriptive
...
text
...
next
...
to
...
each
...
file.
...
This
...
happens
...
because
...
the
...
IGB
...
QuickLoad
...
site
...
has
...
a
...
file
...
named
...
.htaccess
...
that
...
causes
...
Apache
...
to
...
display
...
this
...
information.
...
So
...
when
...
you
...
add
...
a
...
new
...
file
...
type
...
or
...
a
...
new
...
genome
...
to
...
the
...
QuickLoad
...
site,
...
you
...
also
...
need
...
to
...
add
...
a
...
new
...
Description
...
to
...
the
...
.htaccess
...
file.
...
Open
...
the
...
file
...
in
...
a
...
text
...
editor
...
and
...
add
...
one
...
new
...
line
...
for
...
the
...
genome,
...
the
...
same
...
text
...
you
...
added
...
to
...
the
...
contents.txt
...
file,
...
but
...
with
...
the
...
order
...
to
...
the
...
columns
...
reversed.
...
Use
...
the
...
same
...
text
...
to
...
ensure
...
consistency
...
between
...
what
...
IGB
...
shows
...
in
...
the
...
window
...
title
...
bar,
...
what
...
the
...
HEADER.html
...
title
...
displays,
...
and
...
what
...
appears
...
in
...
the
...
directory
...
description
...
when
...
users
...
view
...
the
...
Web
...
site
...
in
...
their
...
Web
...
browser.
...
For
...
example:
...
| Code Block |
|---|
AddDescription "Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0)" G_gallus_Nov_2011
{code}
* |
Note:
...
Add
...
the
...
new
...
text
...
to
...
the
...
end
...
of
...
the
...
file.
...
Test
...
the
...
new
...
genome
...
Testing
...
is
...
absolutely
...
critical
...
as
...
it
...
is
...
easy
...
to
...
make
...
an
...
error
...
along
...
with
...
way.
...
Plan
...
to
...
spend
...
at
...
least
...
as
...
much
...
time
...
testing
...
as
...
you
...
spent
...
on
...
building
...
the
...
site!
...
Test under the released version of IGB
Download the latest release of IGB from http://www.bioviz.org
...
.
...
Configure
...
data
...
sources
...
under
...
Data
...
Sources
...
tab
...
Click
...
the
...
configure
...
link.
...
- Add
...
- your
...
- local
...
- copy
...
- of
...
- the
...
- IGB
...
- QuickLoad
...
- site
...
- to
...
- your
...
- list
...
- of
...
- data
...
- sources
...
- Remove
...
- all
...
- data
...
- sources
...
- EXCEPT
...
- the
...
- UCSC
...
- DAS1
...
- server
...
- and
...
- your
...
- local
...
- QL
...
- directory
Check that the new genome version appears
In the species menu, you should see the organism's genus, species, and strain listed. When you hover the mouse over the its menu item, you should also see a tooltip reporting the species' colloquial name (in English).
In the genome version menu, you should see the genome version name listed.
If not, edit species.txt
If you don't, this only means that IGB doesn't recognize it. To ensure IGB recognizes the genome, add it to the file species.txt that resides at the top level of the IGBQuickLoad directory, the same level as contents.txt.
species.txt is a tab-separated file in which each line represents synonyms for a genome. The first column should list the full Linnean name for the species; this is what will appear in the species menu. It can include spaces. The second column should list the common (colloquial) name for the species, in English. The next column should contain the IGB geome version minus the data and also minus any numbers at the end of the name. The next column should contain the UCSC genome version, minus the number. The final column should contain the genus and species name joined by an underscore.
For example:
| Code Block |
|---|
Pan troglodytes Chimp P_troglodytes panTro Pan_troglodytes
{code}
h3. Restart IGB and |
Restart IGB and re-test
...
When
...
you're
...
done,
...
restart
...
IGB
...
and
...
check
...
that
...
the
...
species
...
and
...
version
...
are
...
displayed
...
correctly.
...
Use
...
the
...
Species
...
and
...
Genome
...
menus
...
(under
...
Current
...
Sequence
...
tab)
...
to
...
select
...
your
...
new
...
genome
...
Choose
...
your
...
genome
...
version.
...
The
...
chromosomes
...
from
...
your
...
genome.txt
...
file
...
should
...
then
...
appear
...
in
...
the
...
Current
...
Sequence
...
tab.
...
You
...
should
...
also
...
see
...
the
...
corresponding
...
UCSC
...
DAS1
...
data
...
source
...
appear
...
in
...
the
...
Data
...
Sets/Data
...
Sources
...
tree
...
on
...
the
...
left.
...
If
...
this
...
step
...
fails,
...
it
...
may
...
be
...
there
...
is
...
a
...
problem
...
with
...
your
...
genome.txt
...
file.
...
Test
...
that
...
you
...
can
...
load
...
sequence
...
data.
...
Check
...
that
...
IGB
...
can
...
load
...
sequence
...
data
...
from
...
your
...
local
...
2bit
...
file.
...
Visit
...
a
...
chromosome,
...
zoom
...
in,
...
and
...
click
...
Load
...
Sequence.
...
Zoom
...
in
...
to
...
check
...
that
...
the
...
sequence
...
is
...
visible.
...
Note
...
that
...
depending
...
on
...
which
...
sequence
...
file
...
you
...
used,
...
some
...
letters
...
will
...
be
...
lower-case.
...
This
...
is
...
how
...
UCSC
...
masks
...
repetitive
...
or
...
low-complexity
...
sequence.
...
Repeat
...
the
...
above
...
tests
...
using
...
the
...
latest
...
(trunk)
...
version
...
of
...
IGB
...
To
...
get
...
a
...
copy
...
of
...
the
...
trunk,
...
check
...
it
...
using
...
svn
...
from
...
sourceforge
...
OR
...
download
...
it
...
from
...
<a
...
href="http://test.bioviz.org/igb/">the
...
test
...
deployment
...
site
...
for
...
IGB</a>.
...
To
...
get
...
the
...
trunk,
...
follow
...
the
...
Download
...
links.
...
Check
...
the
...
new
...
site
...
looks
...
OK
...
in
...
a
...
Web
...
browser
...
Open
...
the
...
site
...
...
if
...
it's
...
on
...
your
...
local
...
computer)
...
in
...
a
...
Web
...
browser
...
and
...
check
...
that
...
- there
...
- are
...
- no
...
- typos
...
- or
...
- errors
...
- in
...
- the
...
- descriptive
...
- text
...
- next
...
- to
...
- the
...
- new
...
- genome
...
- directory
...
- the
...
- genome
...
- directory
...
- has
...
- a
...
- header
...
- and
...
- all
...
- the
...
- files
...
- are
...
- listed
...
- each
...
- file
...
- has
...
- a
...
- description
...
- all
...
- the
...
- links
...
- in
...
- the
...
- HEADER
...
- file
...
- still
...
- work
...
- (report
...
- any
...
- broken
...
- links
...
- as
...
- a
...
- Jira
...
- issue
...
- and
...
- notify
...
- Ann)
...
If
...
all
...
tests
...
pass
...
on
...
both
...
versions,
...
use
...
svn
...
to
...
check
...
in
...
your
...
changes.
...
These
...
include:
...
- edits
...
- to
...
- contents.txt
...
- addition
...
- of
...
- the
...
- new
...
- genome
...
- directory
...
- addition
...
- of
...
- the
...
- genome.txt
...
- file
...
- for
...
- the
...
- genome
...
- edits
...
- to
...
- species.txt
...
- (possibly)
...
When
...
you're
...
finished,
...
submit
...
a
...
ticket
...
to
...
IGB
...
Jira
...
to
...
request
...
testing
...
of
...
the
...
newly
...
added
...
genome
...
on
...
a
...
test
...
site.
...
If
...
you
...
downloaded
...
the
...
2bit
...
file
...
from
...
UCSC,
...
include
...
a
...
link
...
to
...
the
...
file.
...
If
...
you
...
created
...
it
...
from
...
a
...
fasta
...
file,
...
include
...
a
...
link
...
to
...
the
...
fasta
...
file
...
instead.