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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LEARN ABOUT CENTOS

pk-debuginfo-install

PK-DEBUGINFO-INSTA(1)						  [FIXME: manual]					     PK-DEBUGINFO-INSTA(1)

NAME

       pk-debuginfo-install - Debugging Packages Installer

SYNOPSIS

       pk-debuginfo-install [--help] [--verbose] [--simulate] [--no-depends]

DESCRIPTION

       This manual page documents briefly the pk-debuginfo-install command.

       pk-debuginfo-install is the command line client for installing debuginfo packages.

WHY DO I NEED DEBUGINFO PACKAGES
?
       When a program crashes, it's often useful to send the developer a backtrace which contains symbol names and variable contents, rather than
       memory addresses. To make this possible, extra packages called debug packages can be installed.

OPTIONS

       This program follows the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is included
       below.

       --help
	   Show summary of options.

       --noninteractive
	   Do not be interactive and skip the confirmation before the packages are installed.

       --verbose
	   Show extra debugging information.

       --simulate
	   Don't actually install any packages, only simulate what would be installed.

       --no-depends
	   Do not scan for, or install dependencies of the core packages.

       --quiet
	   Do not display information or progress to the terminal.

RETURN VALUES

       0
	   Success, at least one package was installed

       1
	   Failed with miscellaneous internal error.

       3
	   Failed to get software sources list.

       4
	   Failed to enable software sources.

       5
	   Failed as nothing to do.

       6
	   Failed to find dependent packages.

       7
	   Failed to install.

       8
	   Failed to disable software sources.

SEE ALSO

       pkmon (1).  pkcon(1).

AUTHOR

       This manual page was written by Richard Hughes <richard@hughsie.com>.

COPYRIGHT

       Copyright (C) 2009 Richard Hughes

[FIXME: source] 						   29 July,2009 					     PK-DEBUGINFO-INSTA(1)