Question: how_are_we_stranded_here install issue on Xubuntu
0
gravatar for bertb
4 weeks ago by
bertb10
bertb10 wrote:

Hello,

I am trying to install and run the check_strandedness tool in a Unix shell, but I am encountering an error when installing it. First, I downloaded the clone with…

git clone https://github.com/betsig/how_are_we_stranded_here.git

but when I type the command...

pip install how_are_we_stranded_here

I receive the following error…

ERROR: Could not find a version that satisfies the requirement how_are_we_stranded_here (from versions: none)
ERROR: No matching distribution found for how_are_we_stranded_here

I have the following packages to meet the requirements of how_are_we_stranded_here

kallisto 0.44.0
python 3.8.3
RSeQC

I am also working within a VirtualBox version of Xubuntu.

Any help would be appreciated!

Thank you

sequencing rna-seq assembly • 136 views
ADD COMMENTlink modified 4 weeks ago by RamRS30k • written 4 weeks ago by bertb10

Can you try

pip3 install how_are_we_stranded_here

Also, are you sure the git command succeeded?

ADD REPLYlink written 4 weeks ago by RamRS30k

Hi RamRS - thank you for your reply!

I tried the above command you suggested:

pip3 install how_are_we_stranded_here

but I received the same error output.

Though I think the git command succeeded, as the output was as follows:

Cloning into 'how_are_we_stranded_here'...
remote: Enumerating objects: 112, done.
remote: Counting objects: 100% (112/112), done.
remote: Compressing objects: 100% (86/86), done.
remote: Total 112 (delta 37), reused 94 (delta 20), pack-reused 0
Receiving objects: 100% (112/112), 4.37 MiB | 3.67 MiB/s, done.
Resolving deltas: 100% (37/37), done.
ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by bertb10
3
gravatar for RamRS
4 weeks ago by
RamRS30k
Baylor College of Medicine, Houston, TX
RamRS30k wrote:

I think it might be a platform specific error. I took a look at their known issues and there is one that exactly matches your problem: https://github.com/betsig/how_are_we_stranded_here/issues/1

Given that it is solved there, it should work for you too.

ADD COMMENTlink written 4 weeks ago by RamRS30k

Yes, that suggestion worked and I was able to install - thank you!

ADD REPLYlink written 4 weeks ago by bertb10
1

I've moved my comment to an answer now.

Upvote|Bookmark|Accept

ADD REPLYlink written 4 weeks ago by RamRS30k
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