Installing binary not in repositories (openSUSE 12.3)

English Applications
1

Hi,

I’m entirely new to both Linux in general and openSUSE in particular, so apologies in advance for noobities.

I wanted to install the program Bowtie 2
(Bowtie 2: fast and sensitive read alignment)
I couldn’t find it in the repositories accessed by YaST as default, and searching software.opensuse.org yielded only very old versions, so I downloaded the appropriate binary
(bowtie2-2.1.0-linux-x86_64.zip from Bowtie - Browse /bowtie2/2.1.0 at SourceForge.net)
And extracted it to
/home/ChristianAT/Programs
… And then I read that many programs should preferably be installed to, for instance, /usr/local/bin, although it was not clear why.

  1. What is the advantage of installing in /usr/bin or /usr/local/bin - apart from following conventions?
    1.1) When would I chose /usr/bin rather than /usr/local/bin ?

  2. When installing openSUSE, I made a 20 GB root partition and a 170 GB home partition (and a swap partition). If I install in /[something] rather than /home/[something], do I use up root partition space?

2

The manual in the zip explains why one directory or another after a fashion. As I understand it /usr/local/bin is already in the environment path variable so the application will be started where ever a console is opened. eg /home/name or whatever. OpenSuse doesn’t seem to make much use of /usr/local/bin and the directory is there in case software is installed that does. This saves users having to play with the path.

If you type** echo $PATH** in the console it will show what directories are in the user path.

One maybe simpler way to put it anywhere and create a desktop start up on KDE is to right click the start menu icon and select add application. The bits and pieces are pretty easy to fill in. In this case it looks like run in console has to selected.

Last question - yes you would. The normal reason for creating partitions like that is to control the use of more than one disk. Eg my machine has root on ssd, home on a hard drive and swap and /tmp on another hard drive in 2 separate partitions.

John

3

Thanks John,

echo $PATH revealed that /home/ChristianAT/bin was in my path, so I just moved the files to that directory, such that I had /home/ChristianAT/bin/bowtie2-2.1.0

I need to add an environment variable BT2_HOME abcde fd that points to that directory, is that as simple as copy pasting (BT2_HOME= /home/ChristianAT/bin/bowtie2-2.1.0), without the parantheses, into the end of the .bashrc file in /home/ChristianA, or do I need to do it some other way?

4

Open .bashrc in a text editor paste or otherwise enter the string at the end that should work. Ther are several place you can do that but that file should work. Won’t take effect until you log out and back in.

5

Hmm…

Opened .bashrc in the /home/ChristianAT directory in KWrite, added

BT2_HOME= /home/ChristianAT/bin/bowtie2-2.1.0
at the end, saved and closed, then wrote exit in my only open terminal. Tried

printenv

, but BT2_HOME did not appear on the list. Tried to exit and start again, but both

printenv

and

$BT2_HOME

indicate that there is no such variable. What am I doing wrong?

6

Log out and log back in. that file only runs at the start of a session.

7

Thanks for the reply,

but I just logged out and in again a couple of times, and that didn’t help. Also shut down computer and restarted. I don’t know if that could have done anything, but it didn’t help either.

Do I need to check what files are read at startup, or is there some other possible explanation?

8

try putting it in .profile

oh and you need to use export in a script

ie

export BT2_HOME= /home/ChristianAT/bin/bowtie2-2.1.0

9

Tried copy pasting into .profile, that didn’t work either, then googled a bit more, and found that it was the space after the equation mark that was the problem.

Writing the following in .bashrc does nothing, as far as I can tell:
export BT2_HOME= /home/ChristianAT/bin/bowtie2-2.1.0

Writing this works fine:
export BT2_HOME=/home/ChristianAT/bin/bowtie2-2.1.0

10

Eh, like this. Without the export part. Inattentive morning posting here. :\