gmod-ajax

[Gmod-ajax] Change shebang

[Martin A. H. <ma...@ma...>]

Hello Jbrowsers,


I am working on getting Jbrowse to work on my system.

One annoying thing I notice is the Perl scripts in the bin/ dir:

generate-json.pl
generate-names.pl
gff-to-json.pl
prepare-refseqs.pl

all have a hardcoded path to #!/usr/bin/perl which means that the scripts
will run on the system's perl and not on my locally installed perl - which
has the required Bioperl installed.

Please consider changing the shebang to #!/usr/bin/env perl

Also, I believe that 'use warnings;' in all scripts and modules to invoke
warnings locally allowing more fine grained control are better than calling
perl with -w invoking warnings globally.


Best regards,



Martin

Re: [Gmod-ajax] Change shebang

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

Martin A. Hansen wrote:
> generate-json.pl <http://generate-json.pl>
> generate-names.pl <http://generate-names.pl>
> gff-to-json.pl <http://gff-to-json.pl>
> prepare-refseqs.pl <http://prepare-refseqs.pl>
>
> all have a hardcoded path to #!/usr/bin/perl which means that the 
> scripts will run on the system's perl and not on my locally installed 
> perl - which has the required Bioperl installed.
>
> Please consider changing the shebang to #!/usr/bin/env perl

Done.

http://github.com/jbrowse/jbrowse/commit/79ab79e07be80e480d1d20609813226cc1655131

Also, you appear to have an old version of JBrowse; the names of the 
scripts in the bin/ directory changed a while back.  Did you download it 
recently?  If so, from where?

Regards,
Mitch

Re: [Gmod-ajax] Change shebang

[Martin A. H. <ma...@ma...>]

Hello Mitch,


Thanks for the quick fix.

Jbrowse is missing a version/revision number for reporting
questions/features/bugs? How can I tell you what version I have?

I got the code from http://github.com/jbrowse/jbrowse, and I am currently
not using the very latest because there has been introduced an evil
dependency on Gbrowse.pm that I have failed to resolve so far.


Cheers,


Martin


On Mon, Oct 19, 2009 at 11:10 PM, Mitch Skinner
<mit...@be...>wrote:

> Martin A. Hansen wrote:
>
>> generate-json.pl <http://generate-json.pl>
>> generate-names.pl <http://generate-names.pl>
>> gff-to-json.pl <http://gff-to-json.pl>
>> prepare-refseqs.pl <http://prepare-refseqs.pl>
>>
>> all have a hardcoded path to #!/usr/bin/perl which means that the scripts
>> will run on the system's perl and not on my locally installed perl - which
>> has the required Bioperl installed.
>>
>> Please consider changing the shebang to #!/usr/bin/env perl
>>
>
> Done.
>
>
> http://github.com/jbrowse/jbrowse/commit/79ab79e07be80e480d1d20609813226cc1655131
>
> Also, you appear to have an old version of JBrowse; the names of the
> scripts in the bin/ directory changed a while back.  Did you download it
> recently?  If so, from where?
>
> Regards,
> Mitch
>