Question: Tools integrated into a pipeline not working on a galaxy instance
gravatar for bankapur
3.0 years ago by
United States
bankapur0 wrote:


I am trying to integrate my own tool into galaxy on a remote server (LSF). I have made myself admin on the instance and work from there. This pipeline runs Trimmomatic, Tophat, Cufflinks, Cufflinks Annotation (and many more). 

I started out small and ran Trimmomatic alone and it failed with a: 

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory.

Galaxy is able to write the run config file and execute the wrapper script but it won't run Trimmomatic (same is the case with Tophat). 

My understanding is that galaxy is able to write all the output in the directory I ask it to (so no permission issues here) but since the tools that I need to leverage are not in galaxy's path it won't execute them (Note: all the tools that I use are included in my pipeline (since it's Perl so: use <tool name>;) and hence I face no issues in running it through the server).

I don't know what the issue here is exactly if it's not the above mentioned hence any inputs or advice from anyone will be highly appreciated.

Also, could someone point me to documentation which helps configure galaxy on LSF? I have tried using the link below:

But the /galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/ that needs to be exported isn't found in the galaxy directory so I am not sure if I am looking at the most current documentation for it.

Thank you,




rna-seq tools config local lsf • 821 views
ADD COMMENTlink modified 3.0 years ago by Nate Coraor3.1k • written 3.0 years ago by bankapur0
gravatar for Nate Coraor
3.0 years ago by
Nate Coraor3.1k
United States
Nate Coraor3.1k wrote:

Hi Asma,

The error you are receiving when trying to run the job suggests that the user you are starting your Galaxy server as does not have access to the directory that Galaxy is attempting to run jobs in. That directory can be specified using the job_working_directory option in config/galaxy.ini and defaults to database/job_working_directory/ in the Galaxy root directory.

Regarding LSF, the path /galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/ is just an example. is not provided by Galaxy, it should be provided by your distributed resource manager, in this case, LSF. If it's not already a part of your LSF installation, you can grab the latest version from Platform/IBM here:

ADD COMMENTlink written 3.0 years ago by Nate Coraor3.1k

I did a chmod 777 on the directory I wanted galaxy to write files to for the meantime. I will configure the job_working_directory in galaxy.ini file from now on. Thank you Nate!

ADD REPLYlink written 3.0 years ago by bankapur0
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