Question: How to leverage on an existing fasta file as a reference genome build (dbkey)
2
gravatar for jchen015
2.6 years ago by
jchen01580
Singapore
jchen01580 wrote:

Hi Guys

I successfully uploaded a hg19.fa (3GB) file onto my local Galaxy.

Am i able to use this file as a reference genome build (dbkey) to perform visualization of a .bam file?

I am doing it right now but it seems like there are some erroneous error..

This is the image for adding custom build ( https://www.dropbox.com/s/i69dmulcaz9ojhr/adding%20custom_build.png?dl=0 )

This is the image that shows I successfully uploaded the 3.2GB hg19.fa file ( https://www.dropbox.com/s/yd90ezyh2lqovt6/hg19.png?dl=0 )

These are the errors ( https://www.dropbox.com/s/9twx8k8mrgbn28x/error.png?dl=0 )...

  • /home/user/galaxy-dist/database/job_working_directory/000/81/galaxy_81.sh: 17: /home/user/galaxy-dist/database/job_working_directory/000/81/galaxy_81.sh: Syntax error: "(" unexpected
    
  • /home/user/galaxy-dist/database/job_working_directory/000/79/galaxy_79.sh: 17: /home/user/galaxy-dist/database/job_working_directory/000/79/galaxy_79.sh: Syntax error: "(" unexpected
    

When i drill into the directory of /home/user/galaxy-dist/database/job_working_directory/000/ , it does not have 81 or 79 as a folder. The only available folder is just 28 and 29 (as shown here: https://www.dropbox.com/s/m9d4o86ymhynhab/28_29.png?dl=0 ).

 

Anyone happen to know the rational behind it?

ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by jchen01580
1
gravatar for jchen015
2.5 years ago by
jchen01580
Singapore
jchen01580 wrote:

Anyway guys, the problem is solved.

 

Please reference this article for more information.

https://wiki.galaxyproject.org/VisualizationSetup?action=show&redirect=Visualization+Setup#Get_genome_chromosome_length_files

 

Regards,

julius

ADD COMMENTlink written 2.5 years ago by jchen01580

Glad to hear that!

ADD REPLYlink written 2.5 years ago by Martin Čech ♦♦ 4.0k
2
gravatar for Daniel Blankenberg
2.6 years ago by
Daniel Blankenberg ♦♦ 1.6k
United States
Daniel Blankenberg ♦♦ 1.6k wrote:

Trackster requires a .len file, but this Data Manager will only create a len file for a new genome build. If you are just fetching the fasta genome, a len file will not be created, so it will not be selectable in trackster.

ADD COMMENTlink written 2.6 years ago by Daniel Blankenberg ♦♦ 1.6k

Hi Daniel

Thanks for the reply. Appreciate it.

This means using a Data Manager wouldnt solve my intention to get a (.bam and .sam) file up for visualization on my local Galaxy ?

Regards,

Julius
 

ADD REPLYlink written 2.6 years ago by jchen01580
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

Try using this Data Manager to install a reference genome instead. It will set up the dependencies for a dbkey.
https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta

Then you can proceed to using other Data Managers to create indexes, etc.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson22k

Hi Jennifer.

Thanks for the reply.

I have already installed the tool and created the dbkey and reference genome as what you recommended me. (This is the screenshot: https://www.dropbox.com/s/wvgvsa9j3gk7k5j/DBKey_ReferenceNGenome.png?dl=0 ).

After which I clicked on Visualization tab, there is still no reference genome build (dbkey) available. (This is the screenshot: https://www.dropbox.com/s/2t2awuu97ekh7yu/problem.png?dl=0 ).

 

What else do i have to do? All I wanted is to have the same functionality of the public galaxy server of allowing my users to select hg19 as the reference genome build for visualizing (.bam) files....

 

Regards,

Julius

ADD REPLYlink written 2.6 years ago by jchen01580

Hi Julius,

Could you provide a few more details about your local? There is a specific file used by Trackster that should be created by this DM and it is not being found. You restarted you server, I assume, after the database update. If not, try that first, then if still a problem, send us this info:

1. Which distribution are you running?

2. What changes have you made so far? The advanced config for locals is linked from http://getgalaxy.org. Is this what you used? The more details you can provide, the better, while maintaining privacy (do not post passwords, etc).

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson22k

Hi Jen

Yes, I restarted my server. May I know what file was missing and how can i get it ?

 

With reference to what distribution i am using, i executed the hg incoming command on my Terminal :

user@user-Aspire-4755:~/galaxy-dist$ hg incoming
comparing with https://bitbucket.org/galaxy/galaxy-dist/
searching for changes
changeset:   16101:852e7e14fab2
branch:      stable
parent:      16098:ca653e8d044d
user:        Daniel Blankenberg <dan@bx.psu.edu>
date:        Wed Feb 11 16:50:25 2015 -0500
summary:     Fix for resetting repository metadata in the toolshed via UI (pass resetting_all_metadata_on_repository=True flag).

changeset:   16102:8e264f9103b5
branch:      stable
user:        Daniel Blankenberg <dan@bx.psu.edu>
date:        Wed Feb 11 17:31:49 2015 -0500
summary:     Always add sample file info to metadata, not only during initial creation..

changeset:   16103:81fc2eddcad8
branch:      stable
user:        Daniel Blankenberg <dan@bx.psu.edu>
date:        Wed Feb 11 17:36:05 2015 -0500
summary:     When resetting repository metadata in the toolshed, don't overwrite the already set relative_install_dir.

changeset:   16104:71054665755b
branch:      stable
parent:      16100:f1c89c016624
parent:      16103:81fc2eddcad8
user:        Martin Cech <cech.marten@gmail.com>
date:        Thu Feb 12 11:42:29 2015 -0500
summary:     Merged in dan/galaxy-central-prs/stable (pull request #667)

changeset:   16105:6b07e029e315
branch:      stable
parent:      16055:1b96d3a4ff28
user:        Dannon Baker <dannon.baker@gmail.com>
date:        Thu Feb 12 07:57:51 2015 -0500
summary:     Fix at least one error with zipfile downloads and file permissions not being set correctly.

changeset:   16106:1864b26da065
branch:      stable
user:        Dannon Baker <dannon.baker@gmail.com>
date:        Thu Feb 12 08:28:37 2015 -0500
summary:     Fix path manipulation during fetch_eggs.  This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors.  Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers.

changeset:   16107:dd8c3520ccbe
branch:      stable
user:        Dannon Baker <dannonbaker@me.com>
date:        Thu Feb 12 10:34:51 2015 -0500
summary:     Fix path insertion vs appending of <galaxy>/lib for all scripts.

changeset:   16108:a6e9a1d72674
branch:      stable
parent:      16104:71054665755b
parent:      16107:dd8c3520ccbe
user:        Nate Coraor <nate@bx.psu.edu>
date:        Thu Feb 12 13:20:29 2015 -0500
summary:     Merged in dannon/galaxy-central/stable (pull request #668)

changeset:   16109:cc6774fcfed1
branch:      stable
user:        Nate Coraor <nate@bx.psu.edu>
date:        Fri Feb 13 09:00:30 2015 -0500
summary:     Update tag latest_2015.01.13 for changeset a6e9a1d72674

changeset:   16110:09bc07ada38d
branch:      stable
parent:      16095:32e4527bab2d
user:        martenson <cech.marten@gmail.com>
date:        Mon Feb 09 18:16:43 2015 -0500
summary:     one more batch of escape fixes, mostly amending c2bed0a496f8

changeset:   16111:1242b5eb9e63
branch:      stable
user:        martenson <cech.marten@gmail.com>
date:        Tue Feb 10 12:03:19 2015 -0500
summary:     removed unnecessary escapes

changeset:   16112:572aa15bdb08
branch:      stable
user:        martenson <cech.marten@gmail.com>
date:        Tue Feb 10 12:48:53 2015 -0500
summary:     remove incidentally added line

changeset:   16113:6d62105ccb7b
branch:      stable
parent:      16109:cc6774fcfed1
parent:      16112:572aa15bdb08
user:        martenson <cech.marten@gmail.com>
date:        Mon Feb 16 13:56:59 2015 -0500
summary:     Merge

changeset:   16114:d677cb314dcc
branch:      stable
tag:         latest_2015.01.13
user:        martenson <cech.marten@gmail.com>
date:        Mon Feb 16 14:00:52 2015 -0500
summary:     back off some over escaping when uploading capsule

changeset:   16115:02ddea42faad
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Tue Feb 17 09:00:22 2015 -0500
summary:     Update tag latest_2015.01.13 for changeset d677cb314dcc

user@user-Aspire-4755:~/galaxy-dist$

 

With reference to what changes I did so far, I installed various tools and packages like:

  1. HTSeq-Count (Because I want to count the number of map readings)
  2. Bioblend (Because I run scripts with Galaxy API)
  3. Bowtie2 (Just trying out for fun)
  4. Samtools (To Visualize and upload .bam and .sam files)
  5. Bedtools (Because there was once during visualization, the error states Bedtool wasnt installed)
  6. Data Manager tools (as shown here: https://www.dropbox.com/s/mz7micga1a4r6is/asd.png?dl=0)

These are pretty much the core activities I performed on the local Galaxy.

Hope it helps....

Regards,

Julius

ADD REPLYlink written 2.6 years ago by jchen01580
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