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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Cannot open perl script #116

Closed Chloisf closed 4 years ago

Chloisf commented 4 years ago

Hello, I am sorry to ask a question that might be trivial. I am a begginer in bioinformatics and trying to learn how to use NOVOPlasty using the test files. I downloaded the mitochondrial test files and put them in the same directory as the NOVOPlasty3.7.2.pl file. When I type perl NOVOPlasty3.7.2.pl -c config_mito_test.txt in the terminal I get this error Can't open perl script "NOVOPlasty3.7.2.pl": No such file or directory. I don't understand why since I put everything in the same directory, in which I am in the terminal.

I would be very grateful if someone has an idea to fix this problem! Thank you!

ndierckx commented 4 years ago

Hi, are you on a Windows? If could be Perl is not installed yet? https://www.perl.org/get.html

Chloisf commented 4 years ago

Hello! Thank you for answering. Yes I am on Windows. I also wondered if it was about Perl. I checked with perl -v and it appears I do have pearl installed as this is what it shows This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

ndierckx commented 4 years ago

can you show a screenshot of your terminal? Because I don't know what's wrong, if it doesn't find the perl file, it means you are doing something wrong

Chloisf commented 4 years ago

Hello, Thank you! Please find the screenshot below.

screenshotterminalnovoplasty

ndierckx commented 4 years ago

Hi, It's because you have .txt behind all your files... You did use the download button on github the download the zipped file or not? Because I had a user before who got the html scripts of each of the files in stead of downloading it

Chloisf commented 4 years ago

Hi! Oooh that is right. Indeed I individually downloaded each file by clicking download and then download it by right clicking on the newly opened page displaying the file. Thank you for spotting the error, next time I will know! I downloaded the whole NOVOPlasty-master file, unzip it and put it in my directory (chloisf on the screenshot) then tried again. This time the pl file is indeed displayed as pl and not pl.text. However e as I try to run it I have a new error Can't open perl script "NOVOPlasty3.7.2.pl": Permission denied. I'm sorry I think it's still a bit blurry for me how to download and where to put the files...

ndierckx commented 4 years ago

If you don't have permission on your cluster to run anything, I can't help you there. You should contact the administrator