Question: HMMER installed with conda: no tutorial folder
0
gravatar for Wilber0x
12 months ago by
Wilber0x10
Wilber0x10 wrote:

I am trying to use HMMER for the first time. I installed it as per instructions in the user guide, using anaconda:

conda install -c bioconda hmmer

However, now I want to run through the tutorial, and there is no tutorial directory in the HMMER directory installed. There are 9 directories or subdirectories installed, none of them labelled tutorial, yet the HMMER user guide clearly states there should be on.

Tap, tap; is this thing on? In the tutorial subdirectory, globins4.sto is an example of a basic Stockholm alignment file. hmmbuild builds a profile from an alignment:

Has anyone encountered a similar isssue? If so how did you work around it?

ADD COMMENTlink modified 12 months ago by xonq20 • written 12 months ago by Wilber0x10
2
gravatar for xonq
12 months ago by
xonq20
xonq20 wrote:

Conda doesn't package code the same way the creator makes it. It basically creates the necessary binaries and preserves their dependencies in its own directory structure. You will have to go into the conda directory $CONDADIR/env/hmmer and search each sub directory for the tutorials folder. There is a chance it won't be there. As @Mensur Dlakic mentioned, you can download them from the website and specifying the tutorial absolute path.

ADD COMMENTlink written 12 months ago by xonq20
0
gravatar for Mensur Dlakic
12 months ago by
Mensur Dlakic7.1k
USA
Mensur Dlakic7.1k wrote:

Not sure what conda does, but if everything else fails you can always download the files directly:

http://hmmer.org/

There is a prominent button there that says "Download source" and after unpacking there will be a tutorial directory.

ADD COMMENTlink written 12 months ago by Mensur Dlakic7.1k

conda is a python environment manager and its repository (channel) bioconda hosts premade environments of bioinformatic software.

ADD REPLYlink written 12 months ago by xonq20
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