Problems adding bulid-in genomes for tophat on local galaxy

Question: Problems adding bulid-in genomes for tophat on local galaxy

4.4 years ago by

Switzerland

bimbam42 • 10 wrote:

Hi,

I have a question regarding tophat2. I would like to add some mammalian
genomes to run tophat2/bowtie2 on my local galaxy.
I tried using this tutorial:
https://wiki.galaxyproject.org/Admin/DataPreparation?action=show&redirect=Admin%2FNGS+Local+Setup
but the genomes do not show up in my galaxy.
What I did:
downloaded the fasta sequences
created the bt2

/opt/galaxy/galaxy-dist/tool-data/genome/bta/bowtie2/
total 6861592
-rw-rw-r-- 1 galaxy galaxy  940461913 25. Jun 15:35 bosTau7.1.bt2
-rw-rw-r-- 1 galaxy galaxy  701168300 25. Jun 15:35 bosTau7.2.bt2
-rw-rw-r-- 1 galaxy galaxy     846251 25. Jun 14:31 bosTau7.3.bt2
-rw-rw-r-- 1 galaxy galaxy  701168294 25. Jun 14:31 bosTau7.4.bt2
-rwxr-xr-x 1 galaxy galaxy 3040960704 25. Jun 14:16 bosTau7.fa
-rw-rw-r-- 1 galaxy galaxy  940461913 25. Jun 16:36 bosTau7.rev.1.bt2
-rw-rw-r-- 1 galaxy galaxy  701168300 25. Jun 16:36 bosTau7.rev.2.bt2


than modified the bowtie2_indices.loc file like this for each dataset:
btabt2	btabt2	Cow(bta7)
/opt/galaxy/galaxy-dist/tool-data/genome/bta/bowtie2/bosTau7

after restarting the galaxy I get no genomes for selection under "use a
built in genome" "Select a reference genome:" is empty

Has anyone suggestions?

tophat galaxy • 1.7k views

ADD COMMENT • link •

modified 4.4 years ago • written 4.4 years ago by bimbam42 • 10

Have you checked that the separator in your loc file are TAB's not spaces?

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

Good point - check this too! Jen

ADD REPLY • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

4.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

First, the path that the data is at has to be accessible by the "galaxy user". Make sure that is true.

Second, the first two columns need to be the same "dbkey" for the genome that you have in your builds.txt file (or the builds tables, depending on which Galaxy version you are running).

Look under the tool "Get Data -> Upload File" for this genome. Has it been added? What did you use for the short name/dbkey (should be a single "word" - no spaces)? In general this is the same as the base name of the genome (so, bosTau7 in your case), so that the genome's dbkey will work with other tools that use it and reference external sites - in particular UCSC for this one. Use that also for the first two columns in this file (exactly, no extra spaces, same capitalization).

Technically the first column is the dbkey and the other is a "display database" metadata attribute, but it is useful to keep these the same unless you have multiple versions of the genome, all using the same dbkey (e.g. subsets of the genome - any other changes will be problematic).

You can check/compare http://usegalaxy.org and our rsync loc files for examples - this genome is included.

Check the builds list in the UI, adjust the loc, restart, and see if that helps. Builds tables are not fully documented in the wiki yet, but we can help with instructions if your genome is not present there.

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 4.4 years ago • written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

4.4 years ago by

bimbam42 • 10

Switzerland

bimbam42 • 10 wrote:

Thanks, I will have a quick check but I think your suggestions will help.

ADD COMMENT • link written 4.4 years ago by bimbam42 • 10

4.4 years ago by

bimbam42 • 10

Switzerland

bimbam42 • 10 wrote:

Hello again.

I still have no luck with the build-in genomes for tophat2.

My files have real TABs and they are accessible for my galaxy user. The first column and the dbkey are the same like in tool-data/shared/ucsc/build.txt. Or do I need to change the build.txt somewhere else? I also see my changes for my genomes if I look under the tool "Get Data -> Upload File" for this genome.

Maybe I need to set up these so called build tables=?

Thanks Jochen

ADD COMMENT • link written 4.4 years ago by bimbam42 • 10

Is your bowtie2 selectbox also empty?

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

it looks like this:

https://www.dropbox.com/s/yevmjp8ix3cks28/tophat2.png

ADD REPLY • link written 4.4 years ago by bimbam42 • 10

But how looks the bowtie2 tool? Can you send me your loc file?

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

https://www.dropbox.com/s/h5jp7svizv9kwdz/bowtie2_indices.loc

ADD REPLY • link written 4.4 years ago by bimbam42 • 10

Can you share the contents of your tool_data_table_conf.xml and shed_tool_data_table_conf.xml? Also, can you check the contents of your data tables under Admin --> View Data Tables Registry?

ADD REPLY • link written 4.4 years ago by Daniel Blankenberg ♦♦ 1.7k

Thanks for you hints: My View Data Tables Registry look good. Same for the tool_data_table_conf.xml file. only the bwa index files are missing

https://www.dropbox.com/s/qeu8ej7fyimoqlx/shed_tool_data_table_conf.xml

https://www.dropbox.com/s/1nn94frhspf2ay2/tool_data_table_conf.xml

bowtie2_indexes

tool-data/bowtie2_indices.loc

/opt/galaxy/galaxy-dist/tool-data

ADD REPLY • link modified 4.4 years ago • written 4.4 years ago by bimbam42 • 10

4.4 years ago by

bimbam42 • 10

Switzerland

bimbam42 • 10 wrote:

Has anyone more hints after having a look at my xml files?

Or is there anything else I could try?

ADD COMMENT • link written 4.4 years ago by bimbam42 • 10

I solved the problem. My tophat2.xml file pointed to a wrong index file name. But thanks for your help.

ADD REPLY • link written 4.4 years ago by bimbam42 • 10

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