samtools for 32-bit local galaxy

Question: samtools for 32-bit local galaxy

14 months ago by

harryln • 10 wrote:

My local galaxy instance tries to make conda to install samtools each time when I load data. Unfortunate 32-bit samtools is not available via conda installation. Indeed I have installed samtools by sudo apt-get install samtools and it locates in /usr/bin. My question is how to let galaxy recognize this installation of samtools and does not install it again? Many thanks in advance.

path local samtools • 495 views

ADD COMMENT • link •

modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by harryln • 10

14 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You need to add Samtools to your PATH. There are a few other posts that describe how to do this. Search posts for "samtools" and "path" to review. Examples:

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson ♦ 25k

Hi, Jen, Many thanks for your reply.

Use $ which -a samtools, the samtools is /usr/bin/samtools. The path by $ echo $PATH is /home/wl/bin:/home/wl/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/wl/miniconda3/bin. But galaxy still does not find samtools. Do I need to explicitly make a link to let galaxy to know where samtools is? If so, how can I do this? By the way, my R installation is in /usr/bin/R ($ which -a R) and galaxy can find and use it. Many thanks again.

ADD REPLY • link written 14 months ago by harryln • 10

You probably need to point to the expected samtools version that the Samtools tool's require.

Try this: https://biostar.usegalaxy.org/p/10055/#10117

ADD REPLY • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k

Dear Jen, I cannot figure out how to sort it out yet. Actually I have nothing to do with samtools. I have found galaxy let conda to install samtools when uploading CSV data files from local machine. It seems that galaxy try to install samtools again and again in a manner of infinite loop, which prevents me go any further. I just stuck here and desperately need to sort out this problem.

ADD REPLY • link written 13 months ago by harryln • 10

Similar posts • Search »