Question: Getting tophat2 ref index when using data_managers
7
gravatar for Nicholas.Blackburn
21 months ago by
Australia
Nicholas.Blackburn140 wrote:

While setting up a local galaxy instance despite having generated a bowtie2 index using the data_manager tools, and having my reference genome appear in the bowtie2 tool reference genome dropdown, it wasn't appearing in the tophat2 tool reference dropdown. Even though the bowtie2 reference index is what is used for tophat2. 

To get around this I did the following: 

- Accessed galaxy instance at the command line level
- Found that at the end of the bowtie2_indices.loc file there was the paths to the bowtie2 indexes for the 2 reference genomes I have and simple transplanted those two lines across to the tophat2 bowtie2_indicies.loc:

tail -n 2 /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc >> /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/5c5517d2a9e9/bowtie2_indices.loc

- Restarted my galaxy instance 

- happy days! Hopefully someone else finds this useful. 

ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson21k • written 21 months ago by Nicholas.Blackburn140
1

Many thanks Nicholas. I think I'd followed the same steps as you - using the data manager to generate the bowtie2 index (for use in tophat2). But couldn't fathom why there was no reference genome available in the drop down.

Followed your workaround - now it's working.

much appreciated.

Simon (GUDMAP www.gudmap.org)

 

ADD REPLYlink modified 21 months ago • written 21 months ago by gudmapdb10

 I also met this problem and right now can not  solve it . I am confused by your instruction. you mean :copy bowtie2_indices.loc from (galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc) to bowtie2_indices.loc (/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/5c5517d2a9e9/bowtie2_indices.loc).Would you like to introduce this to me. Thank you very much!

 

 

 

 

ADD REPLYlink written 20 months ago by biowz0

Assuming you have a file /galaxy in the top directory and that you've generated a bowtie2 index using the data_manager tools (so you should be able to see a reference genome when you look at the bowtie2 tool in galaxy) just do as one line:

tail -n 2 /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc >> /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/5c5517d2a9e9/bowtie2_indices.loc

which will take the final lines specifying the location of the index in bowtie2 index file and add them to the tophat2 index file.

 

 

ADD REPLYlink written 20 months ago by Nicholas.Blackburn140

HI,  Would you like to help me solve this problem? thank you !

ADD REPLYlink written 20 months ago by biowz0
0
gravatar for biowz
20 months ago by
biowz0
United States
biowz0 wrote:

Thank you very much for your help. I installed galaxy and also used data_manager tools to add bowtie2_index. While bowtie2 software can recognize built-in human genome, but tophat2 can not. I think I may misunderstood your instruction till now. I want to tell how I can do it. There is bowtie2_indices.loc ( Path= xxxx@gmail.com/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/tool-data/bowtie2_indices.loc), and the same files is also found under tophat2 files (Path=xxxx@gmail.com/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ae06af1118dc/tophat2/tool-data/bowtie2_indices.loc ) 

I can also find bowtie2_indices.loc(Path=xxxx@gmail.com/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc) and the same bowtie2_indices.loc(Path=xxxx@gmail.com/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ae06af1118dc/bowtie2_indices.loc)

I deleted all of the words in bowtie2_indices.loc in tophat2 (Path=xxxx@gmail.com/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ae06af1118dc/bowtie2_indices.loc) and copy as "tail -n 2 /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc >> /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ae06af1118dc/bowtie2_indices.loc"   

I still failed to find the correct pathway for tophat2. 

 

ADD COMMENTlink written 20 months ago by biowz0
0
gravatar for biowz
20 months ago by
biowz0
United States
biowz0 wrote:

Furthermore,  This is absolute position for  my human bowtie2_index(path=xxxx@gmail.com/galaxy/tool-data/hg19/bowtie2_index) .Open each biwtie2_indices.loc, we can see as follow:

# bowtie2_indices.loc.sample
# This is a *.loc.sample file distributed with Galaxy that enables tools
# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
# First create these data files and save them in your own data directory structure.
# Then, create a bowtie_indices.loc file to use those indexes with tools.
# Copy this file, save it with the same name (minus the .sample), 
# follow the format examples, and store the result in this directory.
# The file should include an one line entry for each index set.
# The path points to the "basename" for the set, not a specific file.
# It has four text columns seperated by TABS.
#
# <unique_build_id>    <dbkey>    <display_name>    <file_base_path>
#
# So, for example, if you had hg18 indexes stored in:
#
#    /depot/data2/galaxy/hg19/bowtie2/
#
# containing hg19 genome and hg19.*.bt2 files, such as:
#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.bt2
#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.bt2
#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.bt2
#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.bt2
#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.bt2
#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.bt2
#
# then the bowtie2_indices.loc entry could look like this:
#
#hg19    hg19    Human (hg19)    /depot/data2/galaxy/hg19/bowtie2/hg19canon
#
#More examples:
#
#mm10    mm10    Mouse (mm10)    /depot/data2/galaxy/mm10/bowtie2/mm10
#dm3    dm3        D. melanogaster (dm3)    /depot/data2/galaxy/mm10/bowtie2/dm3
#
#

 

I wonder that the path like (hg19    hg19    Human (hg19)    /depot/data2/galaxy/hg19/bowtie2/hg19canon) or (/depot/data2/galaxy/hg19/bowtie2/) is not absolute position for genome index. Why bowtie2 software can work, while tophat2 can not. I also change these paths as absolute positions in bowtie2_indices.loc in  tophat2 files. It is still does not work.Would you like to help me and give me some detailed steps, according to my current file position. Thank you very much in advance 

 

 

ADD COMMENTlink written 20 months ago by biowz0

Hello, The same data table is not used by these tools when the indexes are installed on a cloud Galaxy. We will be amending the Bowtie Data Manager to set up both tools (Bowtie & Tophat) in the next revision. Meanwhile, the indexes need to be manipulated in order for them to be available for Tophat. Dan from our team will be responding with instructions shortly (we are working out the best strategy to share here - there are a few methods). Thanks! Jen, Galaxy team

ADD REPLYlink written 20 months ago by Jennifer Hillman Jackson21k

Thank you very much for your great help. After Dan shares the instruction, I will try to add indexes following the instruction. Have a good day! By the way, I do not use cloud galaxy, just local galaxy on my mac.Shall I use some methods to add genome index to run tophat2  on local galaxy? 

ADD REPLYlink modified 20 months ago • written 20 months ago by biowz0

Sorry, I should have been clearer. It is not a local vs cloud issue, but rather using a Data Manager to install genomes/indexes rather than doing it line-command. You are doing it all correctly. More details coming soon. Jen

ADD REPLYlink written 20 months ago by Jennifer Hillman Jackson21k

Hi Jennifer, I think biowz still needs help with this. Are you guys going to offer some suggestions / details / answers?

ADD REPLYlink written 20 months ago by Nicholas.Blackburn140

Thank you for your taking care. I still need your help. I also using terminal command line:

biowzmailustceducndeMacBook-Pro:galaxy biowzmailustceducn$ tail -n 2 /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc>> /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ae06af1118dc/bowtie2_indices.loc

-bash: /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ae06af1118dc/bowtie2_indices.loc: No such file or directory

But I really found this file

ADD REPLYlink written 20 months ago by biowz0

I am sorry to bring you many problem. I uninstall tophat2 and install the two version tophat2 (ae06af1118dc and 5c5517d2a9e9)again. I found that tophat2 never display in "analyze data" list. I found the status  of package_tophat_2_0_14 is "installed missing repository dependencies" How I  can install the dependencies to repair my tophat2? I could use tophat2 previously, only uninstall and re-install, tophat2 is disappeared.  

ADD REPLYlink written 20 months ago by biowz0

Sorry - I can't offer any advice, hopefully Jennifer or another Galaxy project person will respond to you.

ADD REPLYlink written 20 months ago by Nicholas.Blackburn140

Thank you very much for  your  reply. Right now  everything is OK, though I do not know the reason. Fortunately , I can go for next steps. Thank you! Have a good day for both you and Jennifer.

ADD REPLYlink written 20 months ago by biowz0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 76 users visited in the last hour