Installing packages...need help with the basics Post: 302899123

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Top Forums UNIX for Dummies Questions & Answers Installing packages...need help with the basics Post 302899123 by jullee on Sunday 27th of April 2014 07:30:12 AM

04-27-2014

Registered User

Installing packages...need help with the basics

Hello,

I am working in terminal on a Mac OS X 10.9.2. I need to install a series of bioinformatics tools and packages (currently I want to install fastq-tools but downstream I'll need other such as samtools, bwa etc etc.) and will eventually have to be able to do this not only on my mac but also under my user account on a university linux cluster (to a place on the cluster where I have file permissions I guess?).

The instructions for installing fastq-tools reads:

"on most systems, installation is as simple as ./configure && make && make install"..."the only external dependencies are PCRE and zlib"....

I could use clarification on the following:

1) I assume that the steps are to
- download the package from whatever website is hosting it
- unzip it
- cd to that folder in Terminal
- enter the command <<./configure && make && make>>

I assume that I need to do this for each of the dependencies first...

Is this correct?

2) If I follow these steps, where are the executables actually installed? I'm really confused about the whole /usr/bin versus /usr/local/bin thing. How can I see where packages are installed as a default? (I might have inadvertently changed this messing around by now). In fact, when I do this for the dependancies I get errors...

3) I read that if I want to specify a different directory to store the programs in, I can use:

./configure --prefix=/myUnixStuff/programs
make
sudo make install

(why sudo?)

I've done this for one of the dependancies and a bunch of stuff happened but when I open the /myUnixStuff/programs folder, it's empty. Does this mean it failed (I didn't seem to get error messages) or that stuff went somewhere else?

4) Following up from question 3, how does one see all the programs available in PATH to check that an install worked? For some programs it seems you check by typing <<program -V>> but that's not working in this case.

5) Also following up from question 3, if I DO manage to install all the tools I need to one place on my mac, can I simply scp that file over to the linux cluster and expect it to work? (I'm being optimistic here I know)

Sorry for all the questions. I've been searching online for hours and am very lost. If anyone has a straightforward system for installing packages, I'm eager to hear it. I've come across fink and a few other related tools but my comprehension of linux is too poor for me to really understand what those things do....

Thanks

jullee

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plasmapkg

PLASMAPKG(1)							 KDE User's Manual						      PLASMAPKG(1)

NAME

       plasmapkg - Install, list, remove Plasma packages

SYNOPSIS

       plasmapkg [-h, --hash path] [-g, --global] [-t, --type type] [-i, --install path] [-u, --upgrade path] [-l, --list] [--list-types] [-r,
		 --remove name] [-p, --packageroot path] [KDE Generic Options] [Qt Generic Options]

DESCRIPTION

       plasmapkg is a command line tool to install, list, remove Plasma packages.

OPTIONS

       -h, --hash  path
	   Generate a SHA1 hash for the package at "path".

       -g, --global
	   For install or remove, operates on packages installed for all users.

       -t, --type  type
	   The type of package, e.g.  theme, wallpaper, plasmoid, dataengine, runner, layout-template, etc.  [plasmoid].

       -i, --install  path
	   Install the package at "path".

       -u, --upgrade  path
	   Upgrade the package at "path".

       -l, --list
	   List installed packages.

       -r, --remove  name
	   Remove the package named "name".

       -p, --packageroot  path
	   Absolute path to the package root. If not supplied, then the standard data directories for this KDE session will be searched instead.

SEE ALSO

       More detailed user documentation is available from help:/plasma-desktop (either enter this URL into Konqueror, or run khelpcenter
       help:/plasma-desktop).

AUTHORS

       plasmapkg was written by Aaron Seigo<aseigo@kde.org>.

K Desktop Environment						    2012-12-05							      PLASMAPKG(1)