On Mon, Jan 31, 2011 at 11:28 AM, Lincoln Stein <
lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
> Hi Todd, Keiran,
> I'm working on the problem with the "empty Bio::Graphics::FeatureFile base"
> now. The issue is that
gbrowse_metadb_config.pl isn't being passed the
> prefix when it is invoked. This ought to be an easy fix and will be in 2.25.
> Here is the scoop on why
gbrowse_metadb_config.pl requests root privileges.
> Among the various things this script does is to create the user accounts
> database and to fix directory permissions so that uploads and upload sharing
> works properly. Both the database (in the case of using SQLite) and the
> directories need to be writable by the web user in order for things to work
> properly. So the installer requests root privileges in order to set
> ownership. For a non-privileged install I can deactivate all this, but I
> will have to assume that Apache is running under the same user as the person
> who is installing GBrowse. Do you think this is an acceptable condition?
> Lincoln
>
> On Mon, Jan 31, 2011 at 12:24 PM, Todd Harris <
toddwharris-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>>
>> Hi Keiran -
>>
>> Yes, I've noticed this same problem building against a local perl and
>> installing into a non-privileged path. I resolved in the same manner
>> as you.
>>
>> To simplify installation and avoid library conflicts, we maintain all
>> of our gbrowse installations and prerequisites in local paths. This
>> works well but I've also been a little unsettled when the GBrowse
>> installer requests root privileges.
>>
>> I wonder if it might be cleaner to assume a non-privileged, non-system
>> install, loading into system paths only if requested.
>>
>> Todd
>>
>> On Mon, Jan 31, 2011 at 6:50 AM, Keiran Raine <
kr2-5fLPn3lgkryFxr2TtlUqVg@public.gmane.org> wrote:
>> > Hi all,
>> > Just something to note for anyone not using the default system version
>> > of
>> > perl for their gbrowse setup (normally occurs when you have a site wide
>> > perl
>> > version), e.g.:
>> > ~: perl -v
>> > This is perl, v5.8.8 built for x86_64-linux-thread-multi....
>> > ~: /usr/bin/perl -v
>> > This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi....
>> > As we don't have 5.10 as our default perl I run the installation
>> > manually as
>> > follows:
>> > /usr/bin/perl Build.PL --prefix /gbrowse
>> > ./Build
>> > ./Build test
>> > ./Build install
>> > Which results in the following failure when the
gbrowse_metadb_config.pl
>> > script tries to execute:
>> > Updating user account database...
>> > Base class package "Bio::Graphics::FeatureFile" is empty.
>> > (Perhaps you need to 'use' the module which defines that package
>> > first.)
>> > at
>> >
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>> > line 5
>> > BEGIN failed--compilation aborted at
>> >
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>> > line 5.
>> > Compilation failed in require at (eval 5) line 3.
>> > ...propagated at /software/perl-5.8.8/lib/5.8.8/
base.pm line 85.
>> > BEGIN failed--compilation aborted at
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2.pm line 9.
>> > Compilation failed in require at bin/
gbrowse_metadb_config.pl line 6.
>> > BEGIN failed--compilation aborted at bin/
gbrowse_metadb_config.pl line
>> > 6.
>> > If I just ran this manually with the pathed perl I use at the beginning
>> > of
>> > the install process it woks fine:
>> > /usr/bin/perl -c bin/
gbrowse_metadb_config.pl
>> > bin/
gbrowse_metadb_config.pl syntax OK
>> > Hope this is of use to anyone having issues.
>> > Regards,
>> > Keiran Raine
>> > Senior Computer Biologist
>> > The Cancer Genome Project
>> > Ext: 7703
>> >
kr2-5fLPn3lgkryFxr2TtlUqVg@public.gmane.org
>> >
>> >
>> >
>> >
>> > On 30 Jan 2011, at 20:22, Lincoln Stein wrote:
>> >
>> > Hi All,
>> > I have just released GBrowse 2.23 to
>> > CPAN
http://search.cpan.org/~lds/GBrowse-2.23/ and Ssourceforge
>> >
>> > (
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.23/GBrowse-2.23.tar.gz/download).
>> > IMPORTANT: This release corrects a security issue in which the default
>> > users.sqlite user account database could be created in the root
>> > directory
>> > under some circumstances. If you installed versions 2.20-2.22, please
>> > check
>> > for the presence of /users.sqlite and delete it if it is present. Also
>> > check
>> > the ownership of /, because the install process may have set it to
>> > www-data.
>> > This release also corrects some of the "session lock timeout" issues
>> > that
>> > people have been experiencing. Note, however, that certain long
>> > operations,
>> > such as file uploads, will continue to create timeouts for individual
>> > users;
>> > these are usually safe to ignore. Finally, the bug in which the account
>> > "Registration" link is missing has been fixed.
>> > Here are the complete release notes:
>> >
>> > Version 2.23 (bugfix release)
>> > * SECURITY ISSUE: Fixed default SQLite user account database to be
>> > created in /var/www/gbrowse2/databases rather
>> > than in / (root) directory.
>> > * Added an "example_scripts" directory that contains a perl scripts
>> > that
>> > show how to manipulate
>> > sessions, upload custom tracks, and get basic information about
>> > services. This directory accompanies
>> > new REST API documentation located at
>> >
http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
>> > * Fixed missing "registration" link in login dialog. This occurred
>> > when
>> > openid was unavailable.
>> > * Fixed popup dialogs in the "Help" menu so that they appear again.
>> > * Fixed file upload status display to prevent upload details section
>> > from
>> > disappearing when
>> > uploading very small files.
>> > * Tinkered with session settings to minimize session lock timeouts.
>> > * Removed some dangling warnings in the track sharing module.
>> > * Made SQLite the default user account database.
>> >
>> > Lincoln
>> >
>> > --
>> > Lincoln D. Stein
>> > Director, Informatics and Biocomputing Platform
>> > Ontario Institute for Cancer Research
>> > 101 College St., Suite 800
>> > Toronto, ON, Canada M5G0A3
>> > 416 673-8514
>> > Assistant: Renata Musa <
Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
>> >
>> > ------------------------------------------------------------------------------
>> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> > Finally, a world-class log management solution at an even better
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>> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> > February 28th, so secure your free ArcSight Logger TODAY!
>> >
>> >
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>> > Gmod-gbrowse mailing list
>> >
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>> >
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>> >
>> >
>> > -- The Wellcome Trust Sanger Institute is operated by Genome Research
>> > Limited, a charity registered in England with number 1021457 and a compa
>> > ny
>> > registered in England with number 2742969, whose registered office is 2
>> > 15
>> > Euston Road, London, NW1 2BE.
>> >
>> >
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>> > February 28th, so secure your free ArcSight Logger TODAY!
>> >
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>> > _______________________________________________
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>> >
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>> >
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>> >
>> >
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <
Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
>
Scott
On Mon, Jan 31, 2011 at 2:02 AM, Sharat Chandra
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