Reference genome build (hg19 installation)

Question: Reference genome build (hg19 installation)

3.9 years ago by

Singapore

jchen015 • 80 wrote:

Hi guys.

So I basically deposited my data (hg19 , .bam format) onto my local server and when i need to visualize it, it shows that i did not have the visualization tool as stated in the below link.

https://www.dropbox.com/sh/94lasifl5ubmf1r/AABjAF4pL4silzbaI3xNlPeLa?dl=0

Referencing from https://wiki.galaxyproject.org/Admin/DataPreparation , under Bowtie and Tophat section, I followed the instruction and executed the command "bowtie-build -f hg19.fa hg19".

However, the error showed

Settings:
Output files: "hg19.*.ebwt"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 5 (one in 32)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
hg19.fa
Error: could not open hg19.fa
Total time for call to driver() for forward index: 00:00:00
Command: bowtie-build -f hg19.fa hg19

May I know what's the problem guys??

hg19 installation bowtie visualization bowtie2 • 5.6k views

ADD COMMENT • link •

modified 3.8 years ago • written 3.9 years ago by jchen015 • 80

3.9 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

It sounds like perhaps you're not executing the command from the same directory the hg19.fa file is at (since the error message is that it can't open it). Can you make sure you're in the same directory as hg19.fa prior to running this command?

ADD COMMENT • link written 3.9 years ago by Dannon Baker ♦ 3.7k

Could I just ask if I could, in any ways, locate the hg19.fa file?

Or do i need to download it first ?

Sorry for asking this sort of question as I am really confused on the steps to get the visualization genome hg19 installed...

ADD REPLY • link written 3.9 years ago by jchen015 • 80

Yeah, you'd need to download the hg19.fa file first. As I think about this more, it's probably easier to use Data Managers to get this. Let me figure out the right steps and get back to you.

If you wanted to take a look too, the Data Managers information is here: https://wiki.galaxyproject.org/Admin/Tools/DataManagers

ADD REPLY • link written 3.9 years ago by Dannon Baker ♦ 3.7k

Thanks Dannon.

It seems like Data Managers has alot of pre-requisites to get by and I am having difficulty understanding it..

Do you think I can get it through sourceforge or something?

ADD REPLY • link written 3.8 years ago by jchen015 • 80

We're going to work on a quickstart for using Data Managers that'll make things a little easier, but if you wanted to try the first way you were going about, you can get a copy of hg19 here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

*edit: Sorry, I should have clarified. The .2bit file is available there, and with the utility 2bittofa, found here: http://hgdownload.cse.ucsc.edu/admin/exe/ you can create the .fa file.

ADD REPLY • link modified 3.8 years ago • written 3.8 years ago by Dannon Baker ♦ 3.7k

Hey Dannon

i have downloaded both the .2bit file and also the utility 2bittofa. Do you know how should it be executed?

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

Yeah, you can just do (from the command line). Just go to where you downloaded them both in a terminal and do something like:

   twoBitToFa hg19.2bit hg19.fa

ADD REPLY • link written 3.8 years ago by Dannon Baker ♦ 3.7k

I placed both the files in my desktop and i executed the command u mentioned. it shows this error:

julius@julius-Aspire-4755:~$ cd /home/julius/Desktop/
julius@julius-Aspire-4755:~/Desktop$ twoBitToFa hg19.2bit hg19.fa
twoBitToFa: command not found
julius@julius-Aspire-4755:~/Desktop$ which twoBitToFa
julius@julius-Aspire-4755:~/Desktop$ twoBitToFa
twoBitToFa: command not found

The link for my desktop image is here: https://www.dropbox.com/s/2o9jf5p782gdr24/image.png?dl=0

ADD REPLY • link written 3.8 years ago by jchen015 • 80

twoBitToFa is probably not set executable yet; try this: (including the ./ on the second command)

chmod ugo+x twoBitToFa
./twoBitToFa hg19.2bit hg19.fa

ADD REPLY • link written 3.8 years ago by Dannon Baker ♦ 3.7k

hey Dannon

I tried, it seems like this:

julius@julius-Aspire-4755:~$ cd Desktop
julius@julius-Aspire-4755:~/Desktop$ ./twoBitToFa
bash: ./twoBitToFa: Permission denied
julius@julius-Aspire-4755:~/Desktop$ ./twoBitToFa hg19.2bit hg19.fa
bash: ./twoBitToFa: Permission denied
julius@julius-Aspire-4755:~/Desktop$ sudo ./twoBitToFa hg19.2bit hg19.fa
[sudo] password for julius:
sudo: ./twoBitToFa: command not found

Do I have to install any tools before executing this command?

ADD REPLY • link modified 3.8 years ago • written 3.8 years ago by jchen015 • 80

Hey Dannon.

I found a problem, and that is I did not set the files to executable mode.

After setting them up: It has a new error as stated here.

-rwxrwxrwx 1 julius julius 816241703 Jan 18 20:40 hg19.2bit
-rw-rw-r-- 1 julius julius     51198 Jan 27 22:52 image_1.png
-rw-rw-r-- 1 julius julius     46369 Jan 27 22:53 image_2.png
-rw-rw-r-- 1 julius julius    388024 Jan 31 18:48 image.png
drwxrwxr-x 2 julius julius      4096 Jan 27 22:15 Images
drwxr-xr-x 7 julius julius      4096 Dec 29 15:18 samtools-1.1
-rwxrwxrwx 1 julius julius   1322208 Jan 30 17:54 twoBitToFa
-rw-rw-r-- 1 julius julius       184 Jan 31 20:08 workflow_2.py
-rw-rw-r-- 1 julius julius       195 Jan 31 20:12 workflow_3.py
-rw-rw-r-- 1 julius julius       190 Jan 31 20:03 workflow.py
julius@julius-Aspire-4755:~/Desktop$ ./twoBitToFa hg19.2bit hg19.fa
Error writing 50 bytes: Operation not permitted

What is the meaning of this ?

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

sudo twoBitToFa input.2bit output.fa

ADD REPLY • link written 3.6 years ago by ashishchahl • 0

3.8 years ago by

jchen015 • 80

Singapore

jchen015 • 80 wrote:

Does anybody has a solution in this error?

ADD COMMENT • link written 3.8 years ago by jchen015 • 80

I'm really not sure what's going on with your local configuration there -- you should be able to run the utility after making it executable. It looks like it's trying to run but doesn't have privileges to write back to the Desktop. Have you changed the owner of the desktop (or the hg19.fa file) to root or something?

ADD REPLY • link written 3.8 years ago by Dannon Baker ♦ 3.7k

Hey Dannon.

Thanks for your reply.

I see the hg19.fa file is generated on my Desktop now.

How do I get it in place to my Galaxy server?

Do i have to add it in my PATH or something?

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

Yes, now that you have the file you'll need to continue along with the directions https://wiki.galaxyproject.org/Admin/DataPreparation, editing the .loc files and whatnot to tell your galaxy server where to get it.

ADD REPLY • link written 3.8 years ago by Dannon Baker ♦ 3.7k

Hi Dannon.

Basically I followed the steps and I leverages on bowtie on creating the indices. Now they are all under a directory call hg19 inside my Galaxy directory.

Is it true that the only step left is to set up the loc files?

===============

"Setting Up loc Files

Know where the data is
Know where the bowtie_index.loc, bowtie_index_color.loc, and bowtie2_index.loc files comes from and where they should be placed to be used
initially are named /galaxy-dist/tool-data/bowtie_index.loc.sample, (/galaxy-dist/tool-data/bowtie_index_color.loc.sample, and /galaxy-dist/tool-data/bowtie2_index.loc.sample
from the Tool Shed repository
to your Galaxy instance
Follow instructions in sample file to add in rows for each database. One row per database.
Remove the ".sample" from the file name if this is the first time you are using it
Remove any rows for databases that you no longer want to host if you are altering an existing .loc
You can make sure the file was created correctly by restarting the server and opening up the Bowtie/Bowtie2, Bowtie_color, or Tophat/Tophat2 tool, and checking the dropdown menu of genomes. These tools are found in the tool groups NGS: Mapping and NGS: RNA Analysis, unless you custom installed them elsewhere.
Test the new database(s) by running a few sequences that you expect to have hits with default parameters."

=========

I am unable to find my loc files, as mentioned in the steps, it says that the file should be at

"/galaxy-dist/tool-data/bowtie_index.loc.sample,"

but there is none there...

Do i have to generate or something?? Or infact am I at the correct solution to have the reference genome dbkey set up for visualizing hg19 data.

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

It might not be the absolute path /galaxy-dist/tool-data/, but all these .loc.sample files should all be wherever your galaxy installation is, in a subdirectory named tool-data.

ADD REPLY • link written 3.8 years ago by Dannon Baker ♦ 3.7k

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