I'm using perlbrew and I would like to install the latest bioperl version. Should I use cpanm or git?
If git - do I just install as usual (AKA git clone ... then make and build), or should I do anything special?
UPDATE
Specifically, I'm not sure I understand the following expert from BioPerl Using Git manual:
Tell perl where to find BioPerl
(assuming you checked out the code in
$HOME/src; set this in your
.bash_profile, .profile, or .cshrc):
bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
tcsh: $ setenv PERL5LIB "$HOME/src/bioperl-live:$PERL5LIB"
Why is this necesary?
UPDATE 2
Simply exporting the bioperl cloned dir does not effect all the bp_***.pl scripts (which are usually found under /usr/bin/ after a normal Build installation).
I also tried to build from the cloned dir after switching to the correct perl version using perlbrerw, but then it runs cpan shell to install some dependencies which does not seem to work well with perlbrew (as opposed to cpanm).
So, my question remains...
Thanks!
The latest BioPerl is always going to be on GitHub, so git's your answer there. Whether or not you want bleeding edge is another story, but after following the BioPerl mailing list for some time I get the feeling that the developers are more likely to say "install from GitHub" if you have any problems with BioPerl, especially since the most recent version on CPAN is from 2009. There has been a lot of development since then.
As for installing it, I don't see why you couldn't just go ahead and do the standard git clone ... make/build dance once you're using your perlbrew perl, as that's kind of the point of perlbrew. :-)
Update for question update: The blurb about setting PERL5LIB is there because presumably BioPerl doesn't need to be built once you've cloned it via git; it's ready to use straight out of the box. Assuming you haven't cloned it into a directory in #LIB, you need to tell Perl where to find it. You would have to do this whether or not you are using perlbrew.
Essentially the process goes like this:
Clone BioPerl from GitHub.
Make sure you're using your perlbrew-installed Perl.
Set the PERL5LIB environment variable as per the BioPerl instructions.
Run perl -MBio::Perl -le 'print Bio::Perl->VERSION;' to make sure you're using the BioPerl you just checked out.
Looking at the sourcecode, #4 should print out 1.006900, I think (or maybe 1.6.9, I can never keep Perl version numbers straight).
Related
I have perl 5.8.8 installed in /usr/bin/perl
I need to use a later version, so am trying to install another version in a different place.
(nb. I started out trying to install perlbrew but on the linux server I'm using but that's not working - am getting all sorts of certificate problems).
I logged in as root and followed the instructions here, to install perl from source:
http://www.cpan.org/src/
This gave me an install of perl in
/root/localperl/bin/perl
I thought that didn't look right so I copied that the localperl directory to /usr
cp -r localperl/ /usr/
Now I can run a script in my /home/myusername/ directory by using
/usr/localperl/bin/perl
So I guess that looks more normal for an alternate install of perl, though:
a) Am not sure this is correct. So the question is if I stick #!/usr/localperl/bin/perl as the first line in every script, will all be fine?
b) Have no idea what to do to install modules for this new version. So:
i) What to do to build latest versions of modules for this version?
ii) Can I copy across all my existing modules that work with 5.8.8?
(Yes, I did attempt to read the doc and saw there were lots of options for configuring the install, but having tried one or two found this was even more confusing). Any specific help on the above appreciated.
I'm really happy that SourceTree has Mercurial embedded. On the odd occasion I would like to run an hg command from the CLI, like
hg status
To which I get
hg: command not found
Can I make modifications to my environment path to get the command line working for the embedded version, or do I have to install and manage a separate instance of Mercurial if I want to accasionally use the command line?
I'm using SourceTree OS X version 1.7.2
(This might be a superuser question, but I thought this community has a better chance of knowing and responding.)
The binary lies within SourceTree's bundle, in the resources-folder and is called hg_local.
/Applications/SourceTree.app/Contents/Resources/mercurial_local
You might want to alias it somewhere else (like /usr/local/bin) and rename it on the go:
ln -s /Applications/SourceTree.app/Contents/Resources/mercurial_local /usr/local/bin
It might be a better idea to use some package manager and install mercurial from their repositories, eg. Homebrew. This can be done within few minutes and you gain easy access to lots of other command line tools you might want.
# First install homebrew, than run this command
brew install mercurial
I have following Problem.
I want to build Qt5 by my own, to be able to use it with Visual Studio 2012. I followed the instructions in the Qt Wiki.
My problem is that when I try to call init-repository
perl init-repository
I get following error:
Hint: Make sure that Perl is added to the path in front of git since that ships an outdated version (Perl 5.8), which will cause the scripts to fail.
This is because the with git shipped perl version is 5.8.8. It doesn't matter, that I have the newest version installed.
Can someone tell me how to update my perl version inside git, to be able to build Qt5?
Regards
It sounds like you are working on Windows, I assume with some recent version of msysgit.
If you are using the shell that comes with msysgit, then it is likely that the shell has modified your PATH variable to put /bin ahead of /c/path/to/new/perl. You can check this by opening the shell and running echo $PATH or even which perl.
To make the shell use you 'new' perl, you can try the following:
export PATH=/c/path/to/new/perl:$PATH
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.
I have a Linux server that has no access to the internet (access is prevented by a firewall). I would like to install a new Perl. What are my options and what is the best way to do this? The system Perl (included in OS installation) must remain unchanged.
I have been using perlbrew and I think it is the best way to do an online installation. But all the steps involved in perlbrew seem to require internet access: you download it from the net, it downloads new Perl versions from the net etc. and I haven't found a glue how to make it work offline.
If perlbrew is out of question I could build Perl from source into a custom location on the server. I assume that this could end up being complicated, time-consuming and error-prone. And every time I update Perl I have make a new build manually.
There can also be other ways to install that I'm not currently aware of. And of course I could stick with the system Perl but it is an outdated version and I'm already using the new syntax features. Or I could start negotiations to change the firewall policy to allow internet access for perlbrew.
But all the steps involved in perlbrew seem to require internet access
Not if properly configured.
To install perlbrew itself off-line, install the App-perlbrew dist. Following its dependencies manually is a chore, so instead prepare a MiniCPAN mirror (with -p to include Perl dists), take it over to the target machine and configure CPAN to use the local mirror. Run cpan App::perlbrew to install.
After perlbrew is installed, run its mirror command to configure a CPAN mirror into $PERLBREWROOT/Config.pm. Edit this file to change it to the local MiniCPAN mirror. Drop Perl dist tarballs into $PERLBREWROOT/dists/.
Be aware that compiling Perl requires a working C compiler toolchain, and optionally the development files for libdb (BerkeleyDB) and gdbm. (Read the INSTALL file once over, even though perlbrew's autoconfiguration and Perl's configure.SH defaults hide these details from you.)
The compiler toolchain is probably much more difficult to procure off-line, unless the OS installation has already been used before for compiling other C stuff.
There's nothing that special about perlbrew. If you aren't going to use it to download the Perl sources, it's not saving you that much. Once you have the Perl sources, you just need to configure and install it:
% ./Configure -des -Dprefix=/path/to/installation
% make install
Once done, everything for that Perl is under that installation path.
I dislike perlbrew mostly because it hides from people how amazingly simple this task is so they feel like they can't do it on their own.
Have you considered attacking it from a different direction? Keeping this up-to-date is going to be a pain if you have to request internet access each time. Likewise, if you've missed out/misconfigured any packages in your CPAN mirror it's difficult to correct once you're actually trying to use them.
Perhaps just build a small VM with a cut-down linux + perl + modules. Keep that up-to-date at your end and just take the whole lot in on a USB stick. You'd have a known-working easy-to-setup installation.
What I personally do is using git checkout when I'm offline (and not on vacation). Once you have the whole git work directory, it's trivial to build any released version by checking out the tags:
git checkout v5.17.4
git clean -f # cleanup previously compiled .o files etc
sh ./Configure ...
Depending on how you can transfer files to your host, this can be handy, since you you can also setup a private git repo there so other computer can git push new commits to there.