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BIONF / FAS

FAS - Tool for Feature Architecture Similarity calculation
https://bionf.github.io/FAS/
GNU General Public License v3.0
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Issue with TMHMM 2.0c, SignalP 4.1g, and missing SEG in annoTools.txt #27

Open LucyJimenez opened 2 weeks ago

LucyJimenez commented 2 weeks ago

Hi,

I followed the setup instructions as outlined in the wiki to install annotation tools using fas.setup. During the process, I encountered issues when attempting to include TMHMM 2.0c and SignalP 4.1g.

Case 1: TMHMM 2.0c and SignalP 4.1g Installation Error

When I ran the following command:

fas.setup -t ~/annotation_tools

and opted to install TMHMM 2.0c and SignalP 4.1g, I received the following error:

NotADirectoryError: [Errno 20] Not a directory: '/path/to/tmhmm-2.0c.Linux.tar.gz'

Even though I provided the path to the downloaded tar files as requested, the tool expected a directory instead of a tar.gz file, resulting in a failure to proceed with the installation.

Case 2: Running Without TMHMM 2.0c and SignalP 4.1g

To move forward, I re-ran the setup without including TMHMM 2.0c and SignalP 4.1g. The installation completed successfully, but when I checked the annoTools.txt file, SEG was missing.

Here's the content of annoTools.txt:

#linearized
Pfam
#normal
fLPS
COILS2
#checked

It seems that SEG, which is supposed to be provided by default, was not installed or listed in the file.

Could you provide guidance on resolving these issues? Specifically:

  1. Handling the installation of TMHMM 2.0c and SignalP 4.1g.
  2. Ensuring SEG is included in annoTools.txt.

Thank you for your help!

trvinh commented 1 week ago

Hi @LucyJimenez

  1. To install TMHMM and SignalP, you need to provide only the path to the folder containing signalp-4.1g.Linux.tar.gz and tmhmm-2.0c.Linux.tar.gz files, not the paths to those files. For example:
fas.setup -t ~/fas_anno_tools -d ~/src/dtu/

Here I have the two tar.gz files saved in the ~/src/dtu/ folder (/home/vinh/src/dtu/signalp-4.1g.Linux.tar.gz and /home/vinh/src/dtu/tmhmm-2.0c.Linux.tar.gz)

  1. To check the issue with SEG, could you please send me the log of the installation process? You can use the tee command to save the process into a text file and then email me that file. For example:
fas.setup -t ~/fas_anno_tools -d ~/src/dtu/ | tee fas_installation_log.txt

Best, Vinh