Question: Choose version of software (e.g. minimap2) in Linux
0
gravatar for tanya_fiskur
3 months ago by
tanya_fiskur30
tanya_fiskur30 wrote:

Dear all,

The question is the following:

I need to have a newer version of minimap2 on my computer, but also cannot remove the older one because it is a dependency of another program. If I just install the newer version in addition, the older one is still used as default. Is there a way to specify which version I want to use?

Thank you in advance!

unix minimap2 • 165 views
ADD COMMENTlink modified 3 months ago by Mensur Dlakic5.8k • written 3 months ago by tanya_fiskur30
1

Do you use a package manager or did you compile from source?

ADD REPLYlink written 3 months ago by ATpoint36k

The older version was installed as a part of another software installation. Newer one I tried to install by

git clone https://github.com/lh3/minimap2
cd minimap2 && make

as written in their tutorial ( https://github.com/lh3/minimap2 )

Upd. Installing via "conda install minimap2" helped!

ADD REPLYlink modified 3 months ago • written 3 months ago by tanya_fiskur30
3
gravatar for genomax
3 months ago by
genomax85k
United States
genomax85k wrote:

You could look into creating two separate conda environments for the two versions. Activate and use one you need.

Modules is the proper way of doing this for larger systems (clusters etc).

ADD COMMENTlink modified 3 months ago • written 3 months ago by genomax85k

Thank you! I also thought about that. One version (older) is in "base" environment, and another - in "cogent" environment. Just installing them under different environments didn't help. I also tried to remove the location of older minimap from the path, but didn't help either.

I will try to understand the modules thing..

ADD REPLYlink written 3 months ago by tanya_fiskur30

If you are a single user then modules may be overly complex for you to manage.

Just installing them under different environments didn't help.

Can you elaborate on this? As long as you have one environment active you should be able to use that specific version.

ADD REPLYlink written 3 months ago by genomax85k

I tried to install it via

conda install minimap2

... and it worked! I have the needed version. Thank you and ATpoint for comments!

(excuse me, do you know what to press to close the question? I see only the "upvote" buttons).

ADD REPLYlink modified 3 months ago • written 3 months ago by tanya_fiskur30
0
gravatar for Mensur Dlakic
3 months ago by
Mensur Dlakic5.8k
USA
Mensur Dlakic5.8k wrote:

Have you tried running it with full path to the executable? Say, if you have minimap2 in /usr/bin and in /usr/local/bin directories, both of them can stay in the $PATH. Simply run as /usr/bin/minimap2 or /usr/local/bin/minimap2 to select which one you want.

ADD COMMENTlink written 3 months ago by Mensur Dlakic5.8k

I haven't, because I found out another way, but that's an interesting idea, maybe I'll use it later.

ADD REPLYlink written 12 weeks ago by tanya_fiskur30
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