Question: Is their a way to update HtSeq without uninstalling it?
0
gravatar for Rimma
4 weeks ago by
Rimma20
Hebrew University of Jerusalem
Rimma20 wrote:

Is there a command to update the version of HtSeq without uninstalling it and installing again?

rna-seq • 110 views
ADD COMMENTlink written 4 weeks ago by Rimma20
1

How about using conda?

conda search htseq

followed by

conda create -n htseq_new htseq (if you want the latest)

activate the new environment to use latest htseq.

conda activate htseq_new
ADD REPLYlink written 4 weeks ago by genomax70k

I am working on the cluster and there is no conda environment installed... Is there a way without using conda?

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Rimma20
2

You can install conda in user space, your own directories. No root access is needed so it is easy to do. Check the tutorial from @finswimmer I linked above.

If you don't want to do that then you will need to clone/download htseq version you want/need. Install it in your own directory. Modify $PATH to ensure that it is the only (or first thing) in your $PATH to use it.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax70k
1

You could also try with pip if pip is installed.

sudo pip install htseq --upgrade
ADD REPLYlink written 4 weeks ago by Carlo Yague4.6k

Normal user unlikely to have sudo access on cluster.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax70k

We do have but it replies with this quote: "With great power comes great responsibility." :D This cooled down my ardour a bit and I wrote to the user support to update the programme:)

ADD REPLYlink written 4 weeks ago by Rimma20

If they do that it would be the best solution :-)

ADD REPLYlink written 4 weeks ago by genomax70k
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