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Question: what is "your galaxy path" ????
0
gravatar for solo7773
2.4 years ago by
solo7773 • 20
solo7773 • 20 wrote:

HI guys, I am running my local Galaxy on Ubuntu 16.04. Actually, everything is OK but such an user-friendly galaxy with a hard-to-understand messy wiki/manual/tutorial drives me crazy!

I am going to use the iarc MutSpec (also, the user manual is totally messy). I installed MutSpec from Galaxy toolshed successfully. MutSpec depends on ANNOVAR. I download ANNOVAR and export ANNOVAR's perl scripts location to the Ubuntu PATH. I can successfully run these ANNOVAR scripts directly in the Ubuntu Terminal (i.e.$ table_annovar.pl).

BUT, when I implement my job within Galaxy using the MutSpec tool, after I set up the input data, reference genome, and then click execute, unfortunately, an error appears:

ERROR : table_annovar.pl not found. Add annovar scripts to your galaxy path !
/home/zsf/Downloads/executables/shed_tools/toolshed.g2.bx.psu.edu/repos/iarc/mutspec/46a10309dfe2/mutspec/mutspecAnnot_wrapper.sh: line 2: $'\r': command not found /home/zsf/Do

Then I inspected the mutspecAnnot_wrapper.sh, it includes snippet like following

command -v table_annovar.pl >/dev/null 2>&1 || {
        echo "ERROR: table_annovar.pl not found. Add annovar scripts to your galaxy path!";
        return 1;
}

May I know what the "Galaxy path" is? When I searched in the Galaxy web wiki page, it says no records found for my search. !@#$%^& I even have no word to express my feeling. The Galaxy installation instruction says nothing at all about the "Galaxy path".

My local Galaxy directory is /home/zsf/Downloads/executables/galaxy

I run my local Galxy using sh /home/zsf/Downloads/executables/galaxy/run.sh

All in all, if any body knows, please tell me, where to find the "Galaxy home", how to set it for the MutSpec use.

Thanks a lot.

Nan
annovar galaxy • 1.6k views
ADD COMMENT • link •
modified 2.4 years ago by Peter van Heusden • 150 • written 2.4 years ago by solo7773 • 20
4
gravatar for Peter van Heusden
2.4 years ago by
Peter van Heusden • 150
Peter van Heusden • 150 wrote:

"Your galaxy path" in this case is the PATH environment variable available to your Galaxy server. So in your case, table_annovar.pl needs to be in a directory that is in PATH so that Galaxy can run it. So, at the point where you are doing the sh /home/zsf/Downloads/executables/galaxy/run.sh, can you run table_annovar.pl (without specifying its full location)? If not, Galaxy will also not be able to run it.

An alternative to putting table_annovar.pl directly in the Galaxy PATH is to use a dependency resolver to let Galaxy find the script.

ADD COMMENT • link written 2.4 years ago by Peter van Heusden • 150

Thank you Peter. I think your first solution doesn't work on my problem. For your second suggestion, sorry I am new and don't know how to configure the file. First of all, please have a look at my directory structure

|---- /home/zsf/Downloads/executables

|-------- /home/zsf/Downloads/executables/annovar

|------------ /home/zsf/Downloads/executables/annovar/annotate_variation.pl

|------------ /home/zsf/Downloads/executables/annovar/table_annovar.pl

|------------ /home/zsf/Downloads/executables/annovar/......

|-------- /home/zsf/Downloads/executables/galaxy

|------------/home/zsf/Downloads/executables/galaxy/table_annovar.pl

Now, please have a look at my Ubuntu PATH

$ echo $PATH

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/zsf/Downloads/executables/annovar/:/home/zsf/Downloads/executables/galaxy/

Besides, actually, I can run table_annovar.pl without full path in Ubuntu terminal, i.e., I can run using

$ table_annovar.pl

Can you give me more advice?

ADD REPLY • link modified 2.4 years ago • written 2.4 years ago by solo7773 • 20

So with this all in your path, you then go sh /home/zsf/Downloads/executables/galaxy/run.sh ? I think, however, the subshell that Galaxy uses to run the tool does not inherit the path. You could try adding:

PATH=$PATH:/home/zsf/Downloads/executables/annovar/:/home/zsf/Downloads/executables/galaxy/
export PATH

to config/local_env.sh. This gets sourced by Galaxy as it starts up.

ADD REPLY • link written 2.4 years ago by Peter van Heusden • 150

Thank you Peter. With $PATH including the galaxy directory, I can run galaxy by

$ run.sh

but if use sh (or bash) command, I can only run with full path assigned, like follows

$ sh /home/zsf/Downloads/executables/galaxy/run.sh
$ bash /home/zsf/Downloads/executables/galaxy/run.sh

According to your suggestion, no config/local_env.sh exists in my galaxy/config directory. I created a new config/local_env.sh file and added the lines you gave, but unfortunately, it doesn't work either.

ADD REPLY • link modified 2.4 years ago • written 2.4 years ago by solo7773 • 20
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