Question: HISAT2 path problem (I think)
0
gravatar for vaughandy
10 months ago by
vaughandy10
vaughandy10 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 • 386 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson23k • written 10 months ago by vaughandy10

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 REPLYlink written 10 months ago by Jennifer Hillman Jackson23k

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 REPLYlink written 10 months ago by vaughandy10

Maybe this is a Samtools/$PATH problem.

Help:

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

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

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson23k
0
gravatar for vaughandy
10 months ago by
vaughandy10
vaughandy10 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 COMMENTlink written 10 months ago by vaughandy10

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 REPLYlink written 10 months ago by Hotz, Hans-Rudolf1.7k
0
gravatar for vaughandy
10 months ago by
vaughandy10
vaughandy10 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 COMMENTlink written 10 months ago by vaughandy10
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