Question: Can't use cached bed file
gravatar for luciaaheitor
3 months ago by
luciaaheitor20 wrote:


I wanted to have built-in BED files specific to the genome references that I added to my local galaxy, and so I added a table to the Tool Data Table where I included their paths in the loc file. These show up properly on the local data in the admin tab but when I use it on a tool it says that it cannot find the bed file.

Am I approaching this issue incorrectly? How can I have cached BED files in galaxy that can be used in my tools?

Thank you!

tool bed file local galaxy • 187 views
ADD COMMENTlink written 3 months ago by luciaaheitor20
gravatar for Hotz, Hans-Rudolf
3 months ago by
Hotz, Hans-Rudolf1.8k wrote:

I assume, you are selecting the bed files via the 'from_data_table' option (see: ? and you get the files listed?

If so, I guess, the given paths in the data table are not correct?

Regards, Hans-Rudolf

ADD COMMENTlink written 3 months ago by Hotz, Hans-Rudolf1.8k

Yes, in my tool xml I have this to access the bed files:

                <param name="bed" type="select" label="Select BED file according to the built-in genome choosen">
                <options from_data_table="bed_files">
                    <filter type="sort_by" column="2" />
                    <validator type="no_options" message="No BEDs available" />
                <validator type="no_options" message="A built-in BED file is not available for the build associated with the selected input file"/>

Could there be a problem there? When it gives out the options it looks as expected. I added the bed files in a folder in tools-data and I don't think the path is wrong because I tried to paste it directly in the command of the tool to see if that's the case and it worked perfectly so I guess that's not the mistake I have.

ADD REPLYlink modified 3 months ago • written 3 months ago by luciaaheitor20

The files don't need to be in the tool-data folder (or a sub folder). They can be anywhere. The important think is, that they are listed in the 'loc' file (in your case 'bed_files') with their path.

You might also want to check the command galaxy is executing to see whether the path is correct.

ADD REPLYlink written 3 months ago by Hotz, Hans-Rudolf1.8k

The loc file was based on the all_fasta.loc one and the lines with the value, dbkey, name and path aren't commented so I believe that part may be correct. I hope!

I wanted to do as you suggested and check the command but on the details of the tool run the command line section doesn't appear and I can't think of another way to check. Do you have a suggestion on how can I find the command line?

ADD REPLYlink written 3 months ago by luciaaheitor20

...that should be visible, if you are logged in as an admin. Anyway, as an alternative, use the reports tool or check directly in the database, e.g.: select command_line from job where id = 1234;

ADD REPLYlink written 3 months ago by Hotz, Hans-Rudolf1.8k

Hey, thank you so much for helping me. I don't understand why the command line part wasn't showing on the details when I was signed in as admin. I also couldn't get Galaxy Reports to work (probably more newbie issues), so I decided to try and exhaust all my possible ideas to get you an answer to what galaxy was calling in the command line.

In the end I managed to solve my issue and for that matter I'd like to ask the following: when we use tool data table do we always have to link the option to the parameter? To be clearer, I mean this:

ln -s ${source.bed.fields.path} file.bed
ADD REPLYlink written 3 months ago by luciaaheitor20

I am glad you solved the problem

wrt your next question: It is best to ask a new question (with a different subject). Nevertheless, the quick answer is 'No'. but you need to provide more details.

ADD REPLYlink written 3 months ago by Hotz, Hans-Rudolf1.8k

Thank you for still answering my question! Your answer is reasonable and I really wonder what I was doing wrong. Thank you very much for your time and patience

ADD REPLYlink written 3 months ago by luciaaheitor20
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