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Question: picard: command not found
1
gravatar for stefano cardinale
16 months ago by
stefano cardinale • 20
stefano cardinale • 20 wrote:

Hello, I am using the most recent Galaxy release and I have picard installed and working from command line. I also installed it through the Galaxy tool-shed but when I use it I get the following error:

Fatal error: Exit code 127 () /HOME/galaxy/database/jobs_directory/000/6/tool_script.sh: line 9: picard: command not found

I tried what I can think of including setting conda for dependencies resolution (changed galaxy.ini) but I run out of ideas. Any help is appreciated. Thanks!
17_05 conda install local picard • 666 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by stefano cardinale • 20
2

I guess we need more informations here. Can you look at your Galaxy logs while executing this tool. You should see something like tool executed, dependency resolved with ...

ADD REPLY • link written 16 months ago by Bjoern Gruening ♦ 5.1k
0
gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Update:

Picard installs correctly in a default 17_05 (http://usegalaxy.org) without any dependency config changes if Conda is already on your computer/server. I tested with this version of Picard.

Update your Galaxy instance if needed and use the latest Picard suite as well for best results.

Once installed, if you are also installing local genomes, be sure to also install Samtools and create both Samtools and Picard indexes, using Data Managers for all (genome download/install + indexes). Once the tool is functioning/found, it will expect input datasets that are sorted and that have a database metadata attribute assigned.

If there is more troubleshooting to be done, please confirm the Galaxy version, Picard version, and the information that Bjoern requested. Also note if the tool works properly within the Galaxy GUI (through a browser, in a history). If the tool doesn't work there, it will not work line-command.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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