Circos v0.69-9?

[Chih-Horng Kuo]

Hi,

I am trying to install v0.69-9. The installation from either of these two files worked:

http://circos.ca/distribution/circos-0.69-9.tgz

http://circos.ca/distribution/circos-current.tgz

However, when I used "circos -v" to check the version number after installation, both show:

circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026001

Please let me know how to get the "true" v0.69-9.

Thanks! CH

[kobina kobina]

If you are on a Linux machine , then you need to set PATH to your installation directory.

--
You received this message because you are subscribed to the Google Groups "Circos" group.
To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/f86d90e3-0700-4328-851e-b18139800fa2n%40googlegroups.com.

[Chih-Horng Kuo]

Thanks for the quick response. I tried to set PATH by:

export PATH="${PATH}:/usr/local/bin:/usr/local/circos-0.69-9/bin"

but the problem persists.

The installation is on Ubuntu 18.04.

The previous version that I installed was v0.69-6 and it worked okay. I have not installed v0.69-8 before.

The steps I took were:

[/usr/local]$ sudo wget http://circos.ca/distribution/circos-0.69-9.tgz
[/usr/local]$ sudo tar -xzvf circos-0.69-9.tgz
[/usr/local]$ sudo chown -R root:root circos-0.69-9
[/usr/local]$ sudo ln -s /usr/bin/env /bin/env
[/usr/local]$ sudo ln -s /usr/local/circos-0.69-9/bin/circos /usr/local/bin/circos

[/usr/local]$ circos -v

circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026001

[Naman Mangukia]

Dear Chih-Horng Kuo,

You are right.

I have just downloaded the "circos-0.69-9.tgz" (29.8 Mb) from http://circos.ca/software/download/

No need to set a path and all this to check the version, I just extracted the folder and ran the circos executable.

It is showing the same "v 0.69-8" as you have told:

~/Downloads/circos-0.69-9/bin$ ./circos -v

circos | v 0.69-8 | 15 Jun 2019 | Perl 5.022001

Regards,

Naman

To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/acd8fda4-d219-46b7-8b22-fc7c518f3b23n%40googlegroups.com.

[kobina kobina]

First of all  I recommend you avoid the use of symlinks unless it's very necessary.

Before we proceed, enter the command below to find out which path your circos has been set to.

echo $PATH | grep 'circos'

To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/acd8fda4-d219-46b7-8b22-fc7c518f3b23n%40googlegroups.com.

[Chih-Horng Kuo]

Thanks for taking the time. We use symlinks to put all latest version ones in /usr/local/bin, may I ask why this should be avoided?

For the test:

$ echo $PATH | grep 'circos'
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/circos-0.69-9/bin

$ which circos
/usr/local/bin/circos

$ circos -v
circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026001

$ /usr/local/circos-0.69-9/bin/circos -v

circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026001

$ /usr/local/circos-0.69-6/bin/circos -v
circos | v 0.69-6 | 31 July 2017 | Perl 5.026001

what's puzzling is that we have not installed v 0.69-8.

[kobina kobina]

Hi there,

 

There is nothing wrong with using symlinks but if you are going to use it you must be absolutely sure of the links so that it's easy to debug PATh related issue. Back to circos . Download the version you want.

This time don't use symlinks

extract the contents and put in a directory of your choice .

Now  cd to the bin directory of circos

Type pwd

Take note of the path. If lets say after typiing pwd you have  /home/kuo/circos-0.69/bin , then that becomes your path.

Now export that to your system path

echo "export PATH=$PATH:/home/kuo/circos-0.69/bin">>~/.profile

Open a new terminal and issue your circos -v command to confirm

To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/2927a9af-d055-426b-89b7-44428b348been%40googlegroups.com.

[kobina kobina]

Please I am assuming you are using an Ubuntu OS. if not , then let me know so I give you the appropriate command

[Chih-Horng Kuo]

Yes, I am running Ubuntu 20.04.

Just tried what you said, downloaded 0.69-9, installed in a different dir, modified PATH, and it is still showing 0.69-8

The other user in this thread is reporting the same issue, could it be that the version number in circos-0.69-9.tgz was not updated?

[kobina kobina]

One last thing in addition to .profile,

Modify .bashrc file as well.

On Tue, Aug 18, 2020, 5:24 PM Chih-Horng Kuo <chkuo...@gmail.com> wrote:

--

[Naman Mangukia]

Deal All,

There is nothing to do with the PATH setting.

The issue is in the downloaded version.

Rather downloading the 0.69-9 version, while running circos -v inside it, it showed 0.69-8

To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/CAMtcjRX%3DUCOV3czJy%3DKh22AjW28XB1omcjk_3mqkqKTFKn9HEg%40mail.gmail.com.

[Wayne]

Sorry, I had missed your original post.  You have the true v0.69-9. You installed it right. Basically, I think Martin forgot to adjust the version number in the software during the last update.  I tried asking him about it over a year ago (see here , specifically item #2) because I didn't want to update the Circos Binder and CyVerse images with something that might confuse users but never got a response

[Chih-Horng Kuo]

Thanks Wayne, very helpful!