Question: samtools for 32-bit local galaxy
0
gravatar for harryln
10 weeks ago by
harryln0
harryln0 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 • 141 views
ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson23k • written 10 weeks ago by harryln0
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink modified 10 weeks ago • written 10 weeks ago by Jennifer Hillman Jackson23k

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 REPLYlink written 10 weeks ago by harryln0

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 REPLYlink written 10 weeks ago by Jennifer Hillman Jackson23k

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 REPLYlink written 9 weeks ago by harryln0
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