TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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Install KAT from source to user home directory #107

Closed pbravakos closed 5 years ago

pbravakos commented 6 years ago

I am trying to install KAT to my home directory on a server. My home directory /home/username is actually a link to /mnt/homes/username. When i am trying to run ./kat i get the following error: [kat::FileSystemError*] = Could not find suitable directory containing KAT scripts at the expected location: /mnt/home/username.

For a reason it confuses the /mnt/homes/username and the /home/username home folders to create this hybrid /mnt/home/username. I do not have sufficient technical knowledge to solve this problem, so if you can help me solve this problem it would be really nice. Thanks

maplesond commented 6 years ago

I think I may have fixed this in the latest commit on the develop branch. I'm assuming you cloned the repo from git, can you try switching to the develop branch by typing 'git checkout develop', then try re-configuring and re-building?

pbravakos commented 6 years ago

Yes i have cloned the repo from git, and followed your instructions but the issue still remains. If there is a fix in the future please let me know. Thank you

SvitlanaLukicheva commented 6 years ago

Hello,

I have the same problem. I installed KAT in my home directory, let's call it /myhome/myname, I obtained the same error and the displayed directory is /myhome//myhome/myname. I get this error with the latest version of KAT.

bjclavijo commented 5 years ago

hi @pbravakos and @SvitlanaLukicheva , you probably have solved this somehow, but if not, can you give it a go to actually make sure when you are in installing Kat you have your PWD to be in a real path rather than a symlink?

Let me know it this solves your issue.

Best,

bj

SvitlanaLukicheva commented 5 years ago

Hello bjclavijo, thank you for your response! I don't think I used a symlink when I tried the installation. I finally could install KAT using conda.

bjclavijo commented 5 years ago

good, I'll close this then.