Question: Can't use cached bed file
0
gravatar for luciaaheitor
12 weeks ago by
luciaaheitor20
luciaaheitor20 wrote:

Hey,

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 • 163 views
ADD COMMENTlink written 12 weeks ago by luciaaheitor20
1
gravatar for Hotz, Hans-Rudolf
12 weeks ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

I assume, you are selecting the bed files via the 'from_data_table' option (see: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-options) ? 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 12 weeks 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" />
                </options>
                <validator type="no_options" message="A built-in BED file is not available for the build associated with the selected input file"/>
            </param>

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 12 weeks ago • written 12 weeks 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 12 weeks 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 12 weeks ago by luciaaheitor20
1

...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 12 weeks 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 12 weeks ago by luciaaheitor20
1

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 12 weeks ago by Hotz, Hans-Rudolf1.8k
1

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 12 weeks ago by luciaaheitor20
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