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Question: files not found using Galaxy with Pulsar
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gravatar for jay
7 months ago by
jay • 20
jay • 20 wrote:

Hi,

Hoping some can help me with my issue with Pulsar and Galaxy. I have installed tools and some of the tools are failing because it cannot find specific files when running them in Pulsar. All of them works if the destination is set to local without any issue

I have some Examples below:

Kalipso toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.43.1.1 Missing file command.sh

picard missing file picard.jar

DESeq2 Fatal error: cannot open file '/opt/pulsar/files/staging/6516/tool_files/deseq2.R':

Thanks
pulsar galaxy • 227 views
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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by jay • 20
0
gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please see the administrator documentation for how to set up Pulsar:

After reviewing and making adjustments, if you are still having problems, please consider starting up a Gitter chat question and the developers can help you directly. Be sure to note the version of Galaxy in use, the type (local or docker?), and any other relevant configuration details. You can link back to this post to provide basic context.

GalaxyProject at Gitter: https://gitter.im/galaxyproject/Lobby

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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