Question: Reference genome build (hg19 installation)
0
gravatar for jchen015
2.9 years ago by
jchen01580
Singapore
jchen01580 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??

 

 

 

 

 

 

ADD COMMENTlink modified 2.8 years ago • written 2.9 years ago by jchen01580
0
gravatar for Dannon Baker
2.9 years ago by
Dannon Baker3.6k
United States
Dannon Baker3.6k 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 COMMENTlink written 2.9 years ago by Dannon Baker3.6k

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 REPLYlink written 2.9 years ago by jchen01580

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 REPLYlink written 2.9 years ago by Dannon Baker3.6k

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 REPLYlink written 2.9 years ago by jchen01580

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 REPLYlink modified 2.9 years ago • written 2.9 years ago by Dannon Baker3.6k

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 REPLYlink written 2.9 years ago by jchen01580

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 REPLYlink written 2.9 years ago by Dannon Baker3.6k

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 REPLYlink written 2.9 years ago by jchen01580

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 REPLYlink written 2.9 years ago by Dannon Baker3.6k

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 REPLYlink modified 2.9 years ago • written 2.9 years ago by jchen01580

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 REPLYlink written 2.9 years ago by jchen01580

sudo twoBitToFa input.2bit output.fa

ADD REPLYlink written 2.6 years ago by ashishchahl0
0
gravatar for jchen015
2.8 years ago by
jchen01580
Singapore
jchen01580 wrote:

Does anybody has a solution in this error?

ADD COMMENTlink written 2.8 years ago by jchen01580

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 REPLYlink written 2.8 years ago by Dannon Baker3.6k

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 REPLYlink written 2.8 years ago by jchen01580

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 REPLYlink written 2.8 years ago by Dannon Baker3.6k

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 REPLYlink written 2.8 years ago by jchen01580

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 REPLYlink written 2.8 years ago by Dannon Baker3.6k
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