Ubuntu Install - Hard-coded paths to /home/olson/KB/runtime/bin

[davised]

Hi,

I followed the instructions to download the .deb file for ubuntu and installed as instructed.

When I attempted to run rast-create-genome on a FASTA file with my newly sequenced genome, I received an error:

/usr/bin/rast-create-genome: 6: /usr/bin/rast-create-genome: /home/olson/KB/runtime//bin/perl: not found

I opened /usr/bin/rast-create-genome with vim and noticed that there were several hard-coded paths to /home/olson/KB/runtime.

To solve the problem I ran these commands:

cd /usr/bin  
sudo sed -i 's|/home/olson/KB/runtime/|/usr/share/rasttk/runtime/|' rast-*  
sudo sed -i 's|//|/' rast-*

I also had to manually install JSON::RPC::Client, but that is a separate issue easily fixed with cpan.

Seems to be good to go now. I'll update with any other issues.

Regards,

Ed

[olsonanl]

Thank you for the feedback; the .deb building infrastructure is still a little shaky. I'm glad you were able to get things working.

[jotech]

@davised there seems to be a typo in the second command. Should be: sed -i 's|//|/|' rast-*
Worked for me, too. Thank you for pointing this out!

[jotech]

Just realized that there are much more scripts which needed to be fixed (not only files starting with rast-*). To update all installed files:

cd /usr/share/rasttk/deployment/bin
sed -i 's|/home/olson/KB/runtime/|/usr/share/rasttk/runtime/|' *
sed -i 's|//|/|' *

[EthanGladius]

Hi,

I followed the instructions to download the .deb file for ubuntu and installed as instructed.

When I attempted to run rast-create-genome on a FASTA file with my newly sequenced genome, I received an error:

/usr/bin/rast-create-genome: 6: /usr/bin/rast-create-genome: /home/olson/KB/runtime//bin/perl: not found

I opened /usr/bin/rast-create-genome with vim and noticed that there were several hard-coded paths to /home/olson/KB/runtime.

To solve the problem I ran these commands:

cd /usr/bin  
sudo sed -i 's|/home/olson/KB/runtime/|/usr/share/rasttk/runtime/|' rast-*  
sudo sed -i 's|//|/' rast-*

I also had to manually install JSON::RPC::Client, but that is a separate issue easily fixed with cpan.

Seems to be good to go now. I'll update with any other issues.

Regards,

Ed

Hi @davised,

Sorry to revive such an old thread. I cannot cpan JSON::RPC::Client. It returned cannot find a matching namespace. Seems it got deprecated? Do you have any suggestions to an alternative?

[davised]

You need to install this version

https://metacpan.org/release/MAKAMAKA/JSON-RPC-0.96

You can use this as a guide I think. https://www.perl.com/article/4/2013/3/27/How-to-install-a-specific-version-of-a-Perl-module-with-CPAN/

[davised]

Although the authors suggest using this nowadays instead of the seed tk

https://github.com/PATRIC3/PATRIC-distribution

I haven't used it and don't even remember fixing this bug hah

[EthanGladius]

Thanks @davised , will try PATRIC then. Was hoping to use RAST and SEED for FBA modeling. Seems these things get outdated fast.

[olsonanl]

Since the project has turned over from PATRIC to BV-BRC there are updated distributions at https://github.com/BV-BRC/BV-BRC-CLI/releases

I haven't built the debs for 1.041 yet but 1.040 is there and should work for you.

Bob

[cpplyqz]

I typed: cpan MAKAMAKA/JSON-RPC-0.96.tar.gz
And I got :Warning: no success downloading '/home/amax/.cpan/sources/authors/id/M/MA/MAKAMAKA/JSON-RPC-0.96.tar.gz.tmp268924'. Giving up on it.
No external ftp command available

Please check, if the URLs I found in your configuration file
(http://www.cpan.org/) are valid. The urllist can be edited. E.g. with 'o
conf urllist push ftp://myurl/'

Could not fetch authors/id/M/MA/MAKAMAKA/JSON-RPC-0.96.tar.gz
I dont konw why,T-T