I'm good at installing package in Linux environment but newbie to Solaris OS. I need to install Python - libxml2 package to my project. Does the below command also work in Solaris server for installation??
sudo apt-get install libxml2 libxml2-dev
I have tried googling, unfortunately not able to get.
What you proposed is specific to Debian-based Linux distributions.
IMHO, the fastest way would be to download the libxml2 source code in order to compile and install it yourself.
If you're running Solaris 11, then pkg install libxml2 with sufficient privilege would be the right invocation. Determining the right package name is as simple as pkg search with a reasonable query (assuming that you're still connected to the repository from which you installed the system).
If you're running Solaris 10 or older, then you'll need the original install media, plus whatever patches have been issued that intersect SUNWlxml. But frankly, installing from source is probably easier at that point.
Related
I trying to get set up with Variant Effect Predictor (VEP) on the command line. I'm following the setup tutorial but I'm encountering some errors around dependencies. I'm also quite new to the command line so if anyone is able to break down the solution too then I'd be very grateful. Thanks!
Tutorial: https://www.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
VEP requirements: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements
I also have Perl v5.32.1.
What I've done:
I installed dependencies (listed in the requirements page) with the following commands:
- sudo -s cpanm DBI
- sudo -s cpanm Archive::Zip
- sudo -s cpanm DBD::mysql
For DBD:mysql, I got the follwoing message:
--> Working on DBD::mysql
Fetching http://www.cpan.org/authors/id/D/DV/DVEEDEN/DBD-mysql-4.050.tar.gz ... OK
Configuring DBD-mysql-4.050 ... N/A
! Configure failed for DBD-mysql-4.050. See /root/.cpanm/work/1626111140.5937/build.log for details.
Trying it out anyway, I ran perl INSTALL.pl (from the tutorial page) and got the message below. I would like VEP to run in online mode too if possible.
`WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed
http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements
Hello! This installer is configured to install v104 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.
It will also download and install cache files from Ensembl's FTP server.
Checking for installed versions of the Ensembl API...done
Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
- fetching BioPerl
- unpacking ./Bio/tmp/release-1-6-924.zip
ERROR: Unable to unpack file ./Bio/tmp/release-1-6-924.zip without Archive::Extract or tar/unzip/gzip`
You show us this error:
Configure failed for DBD-mysql-4.050. See /root/.cpanm/work/1626111140.5937/build.log for details.
So looking in there will give you more clues about what the problems are. Without that, we can only guess.
But we can make educated guesses. The DBD::mysql distribution comes with a file called DBD::mysql::INSTALL which will talk you through some of the problems you'll find while installing this module.
It's important to note that DBD::mysql is a wrapper around MySQL's client libraries. They are written in C, so you'll need a C compiler installed in order to build DBD::mysql. You'll also need the client libraries and the development versions of the client libraries (for the C header files that you'll need to compile the module). On Ubuntu, those packages are called "libmysqlclient" and "libmysqlclient-dev". If you don't have a C compiler, then you'll want to install "gcc" too.
But this is all getting a bit complicated. There's another, simpler, approach. If you're using the system version of Perl (the version that was installed as part of the operating system and probably lives in /usr/bin/perl) then I'd recommend using the pre-build Ubuntu version of the package, which you can install by running:
$ sudo apt-get install libdbd-mysql-perl
Installing that version uses the OS's own package manager, and the package manager knows which other packages are needed in order for it to work - so it will install those as well.
People will probably complain that you're better off installing the modules from CPAN as it gives you more flexibility and allows you to use more up-to-date packages than the versions from your OS repos. And they're right. But, honestly, if you're a non-Perl programmer who just wants to get an application up and running, this is by far the simplest approach.
(But, as I said above, this is all guesswork as you haven't shared the most important errors with us.)
I am trying to install Monitorix; but I can't seem to overcome certain issues with the required modules.
I have every prerequisite except for three of the perl modules (MIME-Lite, HTTP-Server-Simple, and Config-General). Even though I have installed them using CPAN, I can't seem to use rpm or yum to finish the installation process (I have the monitorix-3.9.0-1.noarch.rpm file downloaded).
Is there something I'm missing, or some way that is much easier to go about this? I started with a bare-bones Centos 7 system, in accordance to the nature of the course I have to do this for. Anything would be helpful, at this point.
Installing with CPAN is not the equivalent of installing them with yum; the installs are not in the RPM Database. Uninstall them and try again with yum, e.g. yum install perl-MIME-Lite.
I'm running Centos 6.7 on my server and am trying to install Erlang/Rabbitmq following these instructions:
Erlang Installation
RabbitMQ Installation
The trouble is that at time of writing these install Erlang 19.0 with RabbitMQ 3.6.3, which leads to a pretty major bug as far as my client who occasionally looks at the management interface to monitor queues is concerned.
The guidance in the error ticket is not to use erlang 19 until RabbitMQ 3.6.4 is released. But how can I install a specific version of Erlang?
These steps worked for me:
Go to the download page here: https://packages.erlang-solutions.com/erlang/
Select your appropriate package -- you can copy/peek the link then download it using wget.
Install it using rpm.
Example:
# Download erlang 19
$ wget http://packages.erlang-solutions.com/site/esl/esl-erlang/FLAVOUR_1_general/esl-erlang_19.0~centos~7_amd64.rpm
# Install
rpm -Uvh esl-erlang_19.0~centos~7_amd64.rpm
You can always build install from source.
Go to the Erlang.org Downloads page, pick your version from the right side.
From there you can follow the instructions. Although they are for Ubuntu, the commands are the same except for the dependencies part where you can use the command below to install what you need:
sudo yum install g++ openssl-devel unixodbc-devel autoconf ncurses-devel
Another option would be to use kerl, which is similar to rvm in some sense and very (very!) easy to use. It will let you install different Erlang versions and switch between them any time you want.
I prefer this approach instead of looking up packages myself (with possible incompatibilities in the dependencies required) or downloading and compiling everything myself every time I want to try a new Erlang version.
While loading necessities into my crouton, apt-get recommended that I install libtemplate-perl. This seemed a jolly idea, and I obeyed.
Reading this answer, I see a fellow traveler install Plack and Starman via CPAN, but then use apt-get to install Dancer.
Minutes before reading said answer, I had installed Dancer via CPAN. And it had worked. It had worked real good!
What happens differently when I install a CPAN package via a non-CPAN package manager? Are there pitfalls I need to be wary of because my libtemplate-perl came from apt-get, or my Dancer came from CPAN?
On Debian or Debian based distros like Ubuntu, CPAN (/usr/bin/cpan utility) installs modules into /usr/local/lib/ by default. And Debian packages keep their files in /usr/share/perl5/ and /usr/lib/perl5/.
It's a better way to choose dh-make-perl tool to package any CPAN distribution not available in your apt repositories, to avoid making mess (serious risk of conflict between apt and CPAN):
dh-make-perl --build --cpan Some::Module
dpkg -i some-module*.deb
Also check out about local::lib and perlbrew.
A lot of tutorials, Stack Overflow answers, walk throughs, etc. will not want to assume that you know how to use /usr/bin/cpan and will instead suggest that you use your system's package manager, which you are more likely to be familiar with.
This is especially true if you are using a tool written in a particular language, but you don't know that language. For example many people wouldn't care whether crouton is written in Perl, Python or Lisp, they just want a tool they can use. Your average Debian or Ubuntu user is more likely to be familiar with apt-get than with cpan.
If you are looking to program in Perl I recommend installing things by cpan, using perlbrew and/or local::lib. If you are just looking to install a tool you can use, I would recommend using apt-get.
Additionally apt-get has the advantage that non-Perl dependencies will be installed automatically. For example the CPAN module XML::LibXML requires that the libxml2 headers are available on the system; the CPAN distribution has no way of stating that as a dependency, and will simply fail on install if it can find the headers to link against. The Debian package can actually specify that libxml2 is a dependency, and will install the dependency automatically for you.
Despite that if you are looking to use XML::LibXML as a Perl programmer, I would recommend installing it with cpan and installing the libxml2 package via apt-get. Having all your Perl modules installed in the same place - again, via perlbrew or local::lib - will help you keep your sanity in the future. CPAN is preferable to apt-get in this case because not all distributions have been packaged for Debian, and so you get a lot more options if you use CPAN directly.
In summary: TIMTOWTDI ;-)
Another difference to mention that I don't see in other answers, is that if you use CPAN to install a module then the module version you get will be set, until you decide to upgrade that module. Whereas, if you use apt and a later version appears in Debian at some point in the future, then apt-get upgrade will update it.
Maybe you want that, maybe you don't. It's neither necessarily an advantage, nor a disadvantage. Simply a difference to be noted.
The good things about apt-get are
that you can uninstall the packages afterwards should you need to
if you are maintaining any number of servers it is quicker to use apt-get as there is no building required
there are definite versions of packages which are tested for compatibility
The downsides are
not necessarily the latest version of packages
not all packages are available
apt-get installs are generally easier and better than cpan because of dependencies alone.
If you are so lucky as to need SOAP::Lite, for example, it is many dozens of dependencies, and a one-line "apt-get install libsoap-lite-perl".
It is sometimes not clear how Perl CPAN names map to their repository package names, but "apt-cache search " is your friend.
Another approach, that can be used for any distro in HOME install as simple user:
Pros
avoid conflicts
up to date version of perl and modules
when you reinstall, you keep your home/perl as-si
you can upgrade all installed modules with $ cpan -r
Cons
you need to upgrade Perl manually
How to
Edit ~/.bashrc or such, and add:
export PERL5LIB=~/localperl/lib/
export PATH=~/localperl/bin:$PATH
Then
source ~/.bashrc
Install latest Perl5 from sources: https://www.cpan.org/src/README.html
Now, you have an isolate Perl installation in your home.
Enjoy the power to install any libs via:
$ cpan -i Whatever::Module
I was using ubuntu 12.04 until 12.10 was released. I used ubuntu for software development and after installing 12.10, i noticed that the perl version (5.14) shipped with 12.10 does not include the Switch.pm module needed while building WebKiT-GTK.
Looking around on the internet i found few suggestions indicating that i should install something call p5-switch from something called ports. I have looked around and was not able to get this done. I am not a perl guy and have no idea where i can get this package.
Can someone please help me as to
1. Where to download the package for ubuntu 12.10
2. In case it is not a .deb, How do i install it.
OR
1. At least be able to downgrade the perl installation to something lower than 5.14
Thanks and Regards
~Sameer
sudo apt-get install libswitch-perl
will install it for you.
"ports" is a *BSD packaging system of sorts, not what you should be looking for.
You can find what package has a particular perl module by going to packages.ubuntu.com, entering Module/Name.pm (in this case, Switch.pm) in the "Search the contents of packages" form and checking "packages that contain files whose names end with the keyword" and selecting the desired distribution, then making sure you ignore false hits like CGI/Switch.pm in the results. Debian has the identical search for its packages at packages.debian.org.
(Note that Switch.pm has serious limitations, was never really intended to be used in production, and should certainly not be used in new code.)
Do make sure you've checked properly that there isn't the Switch module available via apt. If it is available, that's the one you want.
No, then you've two options the longer, correct way and a shorter way that's not quite as clean.
1. Longer
Install cpanm and perlbrew with apt. The perlbrew tool lets you install a complete version of Perl from scratch in a separate directory. Set up a user for your webkit building, run perlbrew as that user, install your perl. Then, use cpanm to install required modules and you are done. A bit of googling will get you step-by-step examples of how to use these tools. If anything goes badly wrong, you can just delete all the files in that user's home directory and start again - all you waste is a little time.
The reason experienced Perl people prefer this is that it keeps the perl you want for webkit-gtk separate from your system perl that ubuntu's packages will expect to be unchanged from the one they ship.
2. Shorter
Install cpanm with apt. As root, run "cpanm Switch" and it will install the Switch.pm package and any dependencies. It will also upgrade any already installed packages it thinks it needs to. This last step is why this option isn't ideal. In the (rare) case when the update isn't compatible with something else on your system uninstalling is fiddly.