Using clinker in windows Cmd shell, only alignement of last name sequences

[CWoudstra]

Hi,
Im new to clinker.
I have tried to use it through the cmd shell of windows.
When I use the command: clinker cluster/865-C1.gbk, 790_C1.gbk 771, 17-D1.gbk -p
it only produces the alignment with the last 2 files.
Also, trying to use the command: clinker cluster/*.gbk -p
gives me the error "no files found".
Any help would be nice :).
Best,
Cedric

[CWoudstra]

This is not very active troubleshooting...
I guess my problem is very minor, but it would be nice to hear about someone...
Or I just stay with EasyFig, it does the job also.

[gamcil]

Hi @CWoudstra, it looks like you are entering the files with spaces and commas, which will get broken up by the command line before clinker sees it - could you try removing the commas and wrapping the file names in speech marks if they have spaces, e.g. clinker cluster/865-C1.gbk cluster/790_C1.gbk "cluster/771, 17.gbk" -p (presuming that's the last file name)

[CWoudstra]

Hi gamcil,
thank you for your answer.
I had a try and adding speech marks did not work.
I entered: clinker cluster/"865-C.gbk" "790_C1.gbk" "771-17-D1.gbk" -p
It aligned only the last 2 files.
I entered: clinker cluster/865-C.gbk cluster/790_C1.gbk cluster/771-17-D1.gbk -p
it did not find the files.

Do you have other suggestions?
What about: clinker cluster/*.gbk
Why is not working to align all gbk files?

Thank you so much for your help,

Cedric

[gamcil]

Just so I'm sure, you are running clinker in a folder which has a folder called cluster inside it containing your GenBank files? Or are your files in the same folder you are running clinker in? If the first command you wrote there works and not the second, I'm guessing it is the latter, in which case you should delete the cluster/ like so:

clinker "865-C.gbk" "790_C1.gbk" "771-17-D1.gbk" -p

You could also give this web server a shot: CAGECAT

[au1510]

Hi @CWoudstra ! Have you managed to use the clinker cluster/*.gbk at the end? Having the same issue here using windows cmd shell...

Thank you for your help,

Audrey

[hungenlai90]

I had similar issues, but I found that running the following command helped. I've installed clinker in Windows Powershell via pip.

Assuming your current directory contains a folder "clusters" containing .gbk files you want to align, run:
clinker .\clusters\. -p

Or you can cd to the "clusters" folder so that your current directory is now "clusters"
cd .\clusters
Then run:
clinker . -p
The dot (.) indicates all files in current directory

Hope that helps!