HISAT2 path problem (I think)

Question: HISAT2 path problem (I think)

22 months ago by

vaughandy • 10 wrote:

Hi all,

Running a local install of Galaxy and HISAT2 keeps spitting back the following error when it's done:

OSError: [Errno 2] No such file or directory

From googling around I think it's a problem with adding samtools to PATH, but for the life of me nothing I try seems to correct it. I'm running Ubuntu 16.04 LTS. Any advice???

path ubuntu samtools hisat2 • 962 views

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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by vaughandy • 10

This looks more like a database problem (are you using the default or have you upgrade with advanced configuration?) or possibly a network problem if the local has a distributed architecture.

Could you clarify the state of your local for both?

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

I'm using the default config. Not sure about the rest of that, I'm just a newby. All I can say is I've been able to install and run a local instance of galaxy, as well as install a few tools (fastq groomer, hisat, cufflinks).

ADD REPLY • link written 22 months ago by vaughandy • 10

Maybe this is a Samtools/$PATH problem.

Help:

https://biostar.usegalaxy.org/p/19938/

https://biostar.usegalaxy.org/p/10055/

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

22 months ago by

vaughandy • 10

vaughandy • 10 wrote:

This is incredibly frustrating. I keep getting this same error. I know I've added samtools to PATH, when I open a terminal and type samtools it works fine. everything else is working fine.

i noticed if I type sudo samtools, then it doesn't work. i'm running the server with the sudo command. so maybe this has something to do with $PATH for sudo?? Is there something different I should do here? I followed the steps here to add the samtools dir to the $PATH

ADD COMMENT • link written 22 months ago by vaughandy • 10

as a quick and dirty solution: have you tried adding the PATH information to the "run.sh" script?

e.g.: PATH=$PATH:/<path_to_sam_binaries>/SAMtools/samtools-x.y.z

Regards, Hans-Rudolf

ADD REPLY • link written 22 months ago by Hotz, Hans-Rudolf • 1.8k

22 months ago by

vaughandy • 10

vaughandy • 10 wrote:

Hi all,

Thanks for your help. I finally got this to work by adding the samtools path to the /etc/sudoers file under the "secure path" section.

Thanks!!

ADD COMMENT • link written 22 months ago by vaughandy • 10

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