gmod-ajax

[Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello


I've managed to install Jbrowse on my linux box, but somehow the tricks that
worked there don't seem to apply to the Mac. What are the minimal set of
Gbrowse libraries required for Jbrowse?

Installing GD with Fink was the only step that worked (see big rant below).

Is there a pre-packaged Gbrowse perl library that I can just download and
put in my PERL5LIB path to get Jbrowse running?

That would really make my day!

Thanks,

Isabelle


<big rant>
I've spent several hours trying to install Gbrowse on my mac (10.5.6) and
can't get it to go past the blasted cpan nightmare. Sorry, had to let my
frustration out. I really hate cpan with a vengance, and it probably knows
it ;-)

Errors are inconsistent: cpan can't install either LWP, or Harness, or GD,
or Compress::Zlib. I've first tried to execute the Gbrowse installer without
any options. It crashes with:

Force getting a BioPerl nightly build; the most recent release is too old

*** Installing BioPerl ***
Downloading bioperl-live...
Can't locate LWP.pm in @INC (@INC contains:
/System/Library/Perl/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
/Library/Perl/5.8.8 /Library/Perl
/Network/Library/Perl/5.8.8/darwin-thread-multi-2level
/Network/Library/Perl/5.8.8 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1)
at /System/Library/Perl/Extras/5.8.8/LWP/Simple.pm line 37.

I tried to install LWP from cpan and get:
Can't make directory /Users/iphan/.cpan/build/YAML-0.68 read+writeable:
Operation not permitted at /System/Library/Perl/5.8.8/CPAN.pm line 966

I understand that error means I shouldn't have run the gbrowse installer
script with 'sudo', but since it won't run otherwise, what the hell am I
supposed to do??! Manually do a chmod of .cpan after each installer crash?

 I've tried pre-installing Bioperl 7 times, from the tarball, from cpan,
from cvs, version 1.6.0, 1.5.x version, dev version (guess that's the same
as downloading from cvs?), bioperl-live. None of them seem to play with the
Gbrowse perl installer:

*** (back in Bioperl Build.PL) ***
Cannot chdir() back to /Users/iphan/.cpan/build/BioPerl-1.6.0: No such file
or directory at Bio/Root/Build.pm line 461.
Couldn't run Build.PL:
/System/Library/Perl/Extras/5.8.8/Module/Build/Compat.pm line 200.
Running make test
  Make had some problems, maybe interrupted? Won't test
Running make install
  Make had some problems, maybe interrupted? Won't install

</big rant>

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[Mitch S. <mit...@be...>]

iphan wrote:
> I've managed to install Jbrowse on my linux box, but somehow the tricks that
> worked there don't seem to apply to the Mac. What are the minimal set of
> Gbrowse libraries required for Jbrowse?
>   

JBrowse perl dependencies are:

========
(required)
bioperl 1.6
JSON

(optional; gives you a performance boost)
JSON::XS
========

You can get JSON and JSON::XS from CPAN.

Also, if you want to display wiggle files, you need libpng with headers; 
I don't know what the story is on OS X here, probably Ian can tell you.  
All I know is that some of my friends have had more success with 
macports than fink (not with JBrowse specifically but in general), but 
that information is a bit old.  You also need a C++ compiler, but it 
sounds like you've got that already.

And that's all.  Specifically, you *don't* need a GBrowse installation.  
It was the case a long time ago that you did, so there may be a page 
somewhere on biowiki.org that still says you do.  If so, please point it 
out; I thought we either deleted those or marked them as obsolete.

Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello Mitch

installing the latest jbrowse using the tar and the zip file fails because
it looks like the dnd directory is missing from the archives: Apache returns
the error

File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
http://localhost/~iphan/jbrowse/index.html

I've tested the old jbrowse and that works fine, so I know I've got all
dependencies sorted out.

I don't have git, so would very much appreciate it if I could use the
alternative downloads.

Thanks,

Isabelle


On 3/15/09 2:29 AM, "Mitch Skinner" <mit...@be...> wrote:

> iphan wrote:
>> I've managed to install Jbrowse on my linux box, but somehow the tricks that
>> worked there don't seem to apply to the Mac. What are the minimal set of
>> Gbrowse libraries required for Jbrowse?
>>   
> 
> JBrowse perl dependencies are:
> 
> ========
> (required)
> bioperl 1.6
> JSON
> 
> (optional; gives you a performance boost)
> JSON::XS
> ========
> 
> You can get JSON and JSON::XS from CPAN.
> 
> Also, if you want to display wiggle files, you need libpng with headers;
> I don't know what the story is on OS X here, probably Ian can tell you.
> All I know is that some of my friends have had more success with
> macports than fink (not with JBrowse specifically but in general), but
> that information is a bit old.  You also need a C++ compiler, but it
> sounds like you've got that already.
> 
> And that's all.  Specifically, you *don't* need a GBrowse installation.
> It was the case a long time ago that you did, so there may be a page
> somewhere on biowiki.org that still says you do.  If so, please point it
> out; I thought we either deleted those or marked them as obsolete.
> 
> Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[Mitch S. <mit...@be...>]

iphan wrote:
> installing the latest jbrowse using the tar and the zip file fails because it looks like the dnd directory is missing from the archives: Apache returns the error
>
> File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
> http://localhost/~iphan/jbrowse/index.html
>   

Two questions:
* The zip file you're using is the one from github, right?

* Does the HTML (index.html) file have a reference to jbrowse_dojo.js?  
Also, there should be a jbrowse_dojo.js file in the jslib/dojo directory.

I used the dojo custom build tools to create a js file (jbrowse_dojo.js) 
that should include all of the JBrowse dojo dependencies, including 
dnd.  That change should make the whole thing a lot faster to load; I've 
tested it with firefox and I think IE but not with safari so far; I'll 
check that later tonight.

As always, if I can look at the installation over the internet I can 
probably diagnose things faster, although given that it's your laptop I 
can see how that would be tough to do.

> I don't have git, so would very much appreciate it if I could use the alternative downloads.
>   

The tar and zip files from github should be the same as what's in the 
git repository, the last time I tried it, it was the same but I haven't 
checked it lately.  When we make a release I'll also put a zip file on 
jbrowse.org.

Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello Mitch

It looks like my problem was an apache issue (apart from the bioperl issue).
I just unpacked the tarball from github and it works like a charm. Apologies
for wasting your time.

I have one question: I am creating one track from a GFF file at a time, e.g.
a CDS track:

./bin/gff-to-json.pl -gff lmajor_chr1.gff3 --cssclass feature --tracklabel
CDS --featlabel

This creates a track that shows the invidual CDSs, as expected, but it also
displays an element that spans the entire chromosome (see attachment). How
do I only display the CDSs without hacking into the json output? Is there
something like a 'skip top parent feature' option?


Thanks

Isabelle

On 3/18/09 7:51 PM, "Mitch Skinner" <mit...@be...> wrote:

> iphan wrote:
>> installing the latest jbrowse using the tar and the zip file fails because it
>> looks like the dnd directory is missing from the archives: Apache returns the
>> error
>> 
>> File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
>> http://localhost/~iphan/jbrowse/index.html
>>   
> 
> Two questions:
> * The zip file you're using is the one from github, right?
> 
> * Does the HTML (index.html) file have a reference to jbrowse_dojo.js?
> Also, there should be a jbrowse_dojo.js file in the jslib/dojo directory.
> 
> I used the dojo custom build tools to create a js file (jbrowse_dojo.js)
> that should include all of the JBrowse dojo dependencies, including
> dnd.  That change should make the whole thing a lot faster to load; I've
> tested it with firefox and I think IE but not with safari so far; I'll
> check that later tonight.
> 
> As always, if I can look at the installation over the internet I can
> probably diagnose things faster, although given that it's your laptop I
> can see how that would be tough to do.
> 
>> I don't have git, so would very much appreciate it if I could use the
>> alternative downloads.
>>   
> 
> The tar and zip files from github should be the same as what's in the
> git repository, the last time I tried it, it was the same but I haven't
> checked it lately.  When we make a release I'll also put a zip file on
> jbrowse.org.
> 
> Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[Mitch S. <mit...@be...>]

iphan wrote:
> It looks like my problem was an apache issue (apart from the bioperl issue).  I just unpacked the tarball from github and it works like a charm.  Apologies for wasting your time.
>   

Your penance is to occasionally answer an OS X related question on the 
mailing list :)

> This creates a track that shows the invidual CDSs, as expected, but it also displays an element that spans the entire chromosome (see attachment). How do I only display the CDSs without hacking into the json output? Is there something like a 'skip top parent feature' option?
>   

There isn't currently such an option; at the moment what you can do is 
create a config file using the Bio::DB::SeqFeature::Store memory adapter 
and use biodb-to-json.pl instead.  You can look at the example config 
file in docs/tutorial/conf_files/volvox.json to get an idea of how it 
should look.

In the GFF, is the chromosome specified using a #sequence-region 
directive or as a GFF line? 
I think that makes a difference although I'm not entirely sure.  Also, 
I've been thinking about adding a command line option to gff-to-json.pl 
that tells it to only process features of a given type.  Would that do 
what you want?

Sorry those CDS images look so awful; they were just an experiment a 
while ago and I never went back and cleaned them up and made them 
consistent.  I don't really know much about how the annotation process 
works, so I've been wondering how often people want to look at CDSs 
outside of gene models.  Do you get CDS features before the gene models 
have been created?

Mitch