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Question: Help local tool wrapper not seeing BWA getting error: sh: bwa: command not found
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gravatar for cstrittmatter
13 months ago by
cstrittmatter • 0
cstrittmatter • 0 wrote:

Help I have created a tool with a local wrapper that uses BWA when I specify the absolute path to BWA it run fine.

/nfs/sw/apps/bwa/bwa-0.7.15/bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat

But when I take out the absolute path

bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat

I get the following error for galaxy

sh: bwa: command not found

And in my requirements tag I have

<requirement type="package" version="0.5.9.ec2595e4d313">bwa</requirement>

And the following

bwa 0.5.9 package Installed

is installed all tools on the galaxy instance are running fine with BWA it is just my manually created tool is not running.

What am I missing in my dependency configuration?

Regards

Charles

galaxy • 490 views
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modified 13 months ago • written 13 months ago by cstrittmatter • 0
0
gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You referenced two different versions of BWA. One when run line command, the other within the script. Just installing the dependencies is not the same as installing the tool itself that uses that dependency (likely the reason why BWA 0.5.9 isn't found).

Maybe switch to using Planemo if not already? https://galaxyproject.org/tools/

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen thanks for catching version but I have run both versions of bwa inside the script with the absolute path and changing the requirements tags to match. And command output I pasted was from the script not command line. It only not runs with the absolute path t BWA for both versions. And I am using Planemo to install and test the tool.

Charles

ADD REPLY • link written 13 months ago by cstrittmatter • 0

What output do you get if you just type "bwa" at the command prompt? Is that path included in the PATH for the galaxy user?

ADD REPLY • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k
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