Gbrowse2.26 non-root install issue

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Gbrowse2.26 non-root install issue

Sean O'Keeffe
Hi All,
I'm trying to get a local install on a Centos 5 system and I'm getting an odd 'can't install into /etc/default' error at Build install stage.
The installed pre-req's are all new as of yesterday incl. bioperl/biographics etc.
Any help or thoughts would be great.

Sean.

My config is as below:

$ ./Build reconfig
NOTE: Run ./Build reconfig to change existing configuration.
Reuse previous configuration as defaults? [y ]n

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/etc/gbrowse2] /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2] /ifs/data/columbia/tm_lab/www/html
Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
Directory for GBrowse's example databases [/var/www/html/gbrowse2/databases] /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2] /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
Internet port to run demo web site on (for demo)? [8000]
Apache loadable module directory (for demo)? [/etc/httpd/modules]
User account under which Apache daemon runs? [apache] www-data
Automatically update Apache config files to run GBrowse? [y]
Automatically update system config files to run gbrowse-slave? [y]


I then run the build which goes smoothly & finally install:
$ ./Build install
NOTE: Run ./Build reconfig to change existing configuration.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/etc/default'
Do not have write permissions on '/etc/default'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529



------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Gbrowse2.26 non-root install issue

Scott Cain
Hi Sean,

Lincoln wrote a few weeks ago about why root is required to install
GBrowse even if you are installing into directories that are writeable
by your account:

 http://gmod.827538.n3.nabble.com/GBrowse-2-23-released-tt2386677.html#a2392535

However, that has to do with user accounts and SQLite, whereas the
contents of /etc/default is slave renderer info.  I suppose that
adding a config option related to that path ought to be added.

Scott


On Wed, Feb 16, 2011 at 11:58 AM, Sean O'Keeffe <[hidden email]> wrote:

> Hi All,
> I'm trying to get a local install on a Centos 5 system and I'm getting an
> odd 'can't install into /etc/default' error at Build install stage.
> The installed pre-req's are all new as of yesterday incl.
> bioperl/biographics etc.
> Any help or thoughts would be great.
>
> Sean.
>
> My config is as below:
>
> $ ./Build reconfig
> NOTE: Run ./Build reconfig to change existing configuration.
> Reuse previous configuration as defaults? [y ]n
>
> **Beginning interactive configuration**
> Directory for GBrowse's config and support files? [/etc/gbrowse2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
> Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2]
> /ifs/data/columbia/tm_lab/www/html
> Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
> Directory for GBrowse's example databases [/var/www/html/gbrowse2/databases]
> /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
> Internet port to run demo web site on (for demo)? [8000]
> Apache loadable module directory (for demo)? [/etc/httpd/modules]
> User account under which Apache daemon runs? [apache] www-data
> Automatically update Apache config files to run GBrowse? [y]
> Automatically update system config files to run gbrowse-slave? [y]
>
>
> I then run the build which goes smoothly & finally install:
> $ ./Build install
> NOTE: Run ./Build reconfig to change existing configuration.
> Building GBrowse
> Files found in blib/arch: installing files in blib/lib into architecture
> dependent library tree
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ERROR: Can't create '/etc/default'
> Do not have write permissions on '/etc/default'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Gbrowse2.26 non-root install issue

Sean O'Keeffe-2
Hi Scott,
answering no the gbrowse_slave update question leads to a build install issue of:

ERROR: Can't create '/etc/httpd/conf.d'
Do not have write permissions on '/etc/httpd/conf.d'

It shouldn't be writing here.
Sean.

On 16 February 2011 12:56, Scott Cain <[hidden email]> wrote:
Hi Sean,

Lincoln wrote a few weeks ago about why root is required to install
GBrowse even if you are installing into directories that are writeable
by your account:

 http://gmod.827538.n3.nabble.com/GBrowse-2-23-released-tt2386677.html#a2392535

However, that has to do with user accounts and SQLite, whereas the
contents of /etc/default is slave renderer info.  I suppose that
adding a config option related to that path ought to be added.

Scott


On Wed, Feb 16, 2011 at 11:58 AM, Sean O'Keeffe <[hidden email]> wrote:
> Hi All,
> I'm trying to get a local install on a Centos 5 system and I'm getting an
> odd 'can't install into /etc/default' error at Build install stage.
> The installed pre-req's are all new as of yesterday incl.
> bioperl/biographics etc.
> Any help or thoughts would be great.
>
> Sean.
>
> My config is as below:
>
> $ ./Build reconfig
> NOTE: Run ./Build reconfig to change existing configuration.
> Reuse previous configuration as defaults? [y ]n
>
> **Beginning interactive configuration**
> Directory for GBrowse's config and support files? [/etc/gbrowse2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
> Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2]
> /ifs/data/columbia/tm_lab/www/html
> Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
> Directory for GBrowse's example databases [/var/www/html/gbrowse2/databases]
> /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
> Internet port to run demo web site on (for demo)? [8000]
> Apache loadable module directory (for demo)? [/etc/httpd/modules]
> User account under which Apache daemon runs? [apache] www-data
> Automatically update Apache config files to run GBrowse? [y]
> Automatically update system config files to run gbrowse-slave? [y]
>
>
> I then run the build which goes smoothly & finally install:
> $ ./Build install
> NOTE: Run ./Build reconfig to change existing configuration.
> Building GBrowse
> Files found in blib/arch: installing files in blib/lib into architecture
> dependent library tree
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ERROR: Can't create '/etc/default'
> Do not have write permissions on '/etc/default'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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|

Re: Gbrowse2.26 non-root install issue

Sean O'Keeffe-2
Sorry for reposting but I'm getting no joy on this:

1)
/opt/perl/bin/perl Build.PL --cgibin=/ifs/data/columbia/tm_lab/so2346/gbrowse_scripts/cgi-bin --conf=/ifs/data/columbia/tm_lab/so2346/gbrowse_scripts/conf --htdocs=/ifs/data/columbia/tm_lab/www/html --tmp=/var/tmp/gbrowse2 --lib=/opt/perl/lib/perl5

2)
./Build install
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/etc/httpd/conf.d'
Do not have write permissions on '/etc/httpd/conf.d'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529

Why is it trying to install there?
Any ideas?

Thanks,
Sean.



On 16 February 2011 13:56, Sean O'Keeffe <[hidden email]> wrote:
Hi Scott,
answering no the gbrowse_slave update question leads to a build install issue of:

ERROR: Can't create '/etc/httpd/conf.d'
Do not have write permissions on '/etc/httpd/conf.d'

It shouldn't be writing here.
Sean.


On 16 February 2011 12:56, Scott Cain <[hidden email]> wrote:
Hi Sean,

Lincoln wrote a few weeks ago about why root is required to install
GBrowse even if you are installing into directories that are writeable
by your account:

 http://gmod.827538.n3.nabble.com/GBrowse-2-23-released-tt2386677.html#a2392535

However, that has to do with user accounts and SQLite, whereas the
contents of /etc/default is slave renderer info.  I suppose that
adding a config option related to that path ought to be added.

Scott


On Wed, Feb 16, 2011 at 11:58 AM, Sean O'Keeffe <[hidden email]> wrote:
> Hi All,
> I'm trying to get a local install on a Centos 5 system and I'm getting an
> odd 'can't install into /etc/default' error at Build install stage.
> The installed pre-req's are all new as of yesterday incl.
> bioperl/biographics etc.
> Any help or thoughts would be great.
>
> Sean.
>
> My config is as below:
>
> $ ./Build reconfig
> NOTE: Run ./Build reconfig to change existing configuration.
> Reuse previous configuration as defaults? [y ]n
>
> **Beginning interactive configuration**
> Directory for GBrowse's config and support files? [/etc/gbrowse2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
> Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2]
> /ifs/data/columbia/tm_lab/www/html
> Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
> Directory for GBrowse's example databases [/var/www/html/gbrowse2/databases]
> /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
> Internet port to run demo web site on (for demo)? [8000]
> Apache loadable module directory (for demo)? [/etc/httpd/modules]
> User account under which Apache daemon runs? [apache] www-data
> Automatically update Apache config files to run GBrowse? [y]
> Automatically update system config files to run gbrowse-slave? [y]
>
>
> I then run the build which goes smoothly & finally install:
> $ ./Build install
> NOTE: Run ./Build reconfig to change existing configuration.
> Building GBrowse
> Files found in blib/arch: installing files in blib/lib into architecture
> dependent library tree
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ERROR: Can't create '/etc/default'
> Do not have write permissions on '/etc/default'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Gbrowse2.26 non-root install issue

Sean O'Keeffe
In reply to this post by Scott Cain
Sorry for reposting but I'm getting no joy on this:

1)
/opt/perl/bin/perl Build.PL --cgibin=/ifs/data/columbia/
tm_lab/so2346/gbrowse_scripts/cgi-bin --conf=/ifs/data/columbia/tm_lab/so2346/gbrowse_scripts/conf --htdocs=/ifs/data/columbia/tm_lab/www/html --tmp=/var/tmp/gbrowse2 --lib=/opt/perl/lib/perl5

2)
./Build install
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

ERROR: Can't create '/etc/httpd/conf.d'
Do not have write permissions on '/etc/httpd/conf.d'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529


On 16 February 2011 12:56, Scott Cain <[hidden email]> wrote:
Hi Sean,

Lincoln wrote a few weeks ago about why root is required to install
GBrowse even if you are installing into directories that are writeable
by your account:

 http://gmod.827538.n3.nabble.com/GBrowse-2-23-released-tt2386677.html#a2392535

However, that has to do with user accounts and SQLite, whereas the
contents of /etc/default is slave renderer info.  I suppose that
adding a config option related to that path ought to be added.

Scott


On Wed, Feb 16, 2011 at 11:58 AM, Sean O'Keeffe <[hidden email]> wrote:
> Hi All,
> I'm trying to get a local install on a Centos 5 system and I'm getting an
> odd 'can't install into /etc/default' error at Build install stage.
> The installed pre-req's are all new as of yesterday incl.
> bioperl/biographics etc.
> Any help or thoughts would be great.
>
> Sean.
>
> My config is as below:
>
> $ ./Build reconfig
> NOTE: Run ./Build reconfig to change existing configuration.
> Reuse previous configuration as defaults? [y ]n
>
> **Beginning interactive configuration**
> Directory for GBrowse's config and support files? [/etc/gbrowse2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
> Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2]
> /ifs/data/columbia/tm_lab/www/html
> Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
> Directory for GBrowse's example databases [/var/www/html/gbrowse2/databases]
> /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
> /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
> Internet port to run demo web site on (for demo)? [8000]
> Apache loadable module directory (for demo)? [/etc/httpd/modules]
> User account under which Apache daemon runs? [apache] www-data
> Automatically update Apache config files to run GBrowse? [y]
> Automatically update system config files to run gbrowse-slave? [y]
>
>
> I then run the build which goes smoothly & finally install:
> $ ./Build install
> NOTE: Run ./Build reconfig to change existing configuration.
> Building GBrowse
> Files found in blib/arch: installing files in blib/lib into architecture
> dependent library tree
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ERROR: Can't create '/etc/default'
> Do not have write permissions on '/etc/default'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
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|

Re: Gbrowse2.26 non-root install issue

Todd Harris
Perhaps try ./Build reconfig and turn off the autoupdate of apache
configuration?

Todd

On Thu, Feb 17, 2011 at 10:31 AM, Sean O'Keeffe <[hidden email]> wrote:

> Sorry for reposting but I'm getting no joy on this:
>
> 1)
> /opt/perl/bin/perl Build.PL --cgibin=/ifs/data/columbia/
> tm_lab/so2346/gbrowse_scripts/cgi-bin
> --conf=/ifs/data/columbia/tm_lab/so2346/gbrowse_scripts/conf
> --htdocs=/ifs/data/columbia/tm_lab/www/html --tmp=/var/tmp/gbrowse2
> --lib=/opt/perl/lib/perl5
>
> 2)
> ./Build install
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ERROR: Can't create '/etc/httpd/conf.d'
> Do not have write permissions on '/etc/httpd/conf.d'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>
> On 16 February 2011 12:56, Scott Cain <[hidden email]> wrote:
>>
>> Hi Sean,
>>
>> Lincoln wrote a few weeks ago about why root is required to install
>> GBrowse even if you are installing into directories that are writeable
>> by your account:
>>
>>
>>  http://gmod.827538.n3.nabble.com/GBrowse-2-23-released-tt2386677.html#a2392535
>>
>> However, that has to do with user accounts and SQLite, whereas the
>> contents of /etc/default is slave renderer info.  I suppose that
>> adding a config option related to that path ought to be added.
>>
>> Scott
>>
>>
>> On Wed, Feb 16, 2011 at 11:58 AM, Sean O'Keeffe <[hidden email]>
>> wrote:
>> > Hi All,
>> > I'm trying to get a local install on a Centos 5 system and I'm getting
>> > an
>> > odd 'can't install into /etc/default' error at Build install stage.
>> > The installed pre-req's are all new as of yesterday incl.
>> > bioperl/biographics etc.
>> > Any help or thoughts would be great.
>> >
>> > Sean.
>> >
>> > My config is as below:
>> >
>> > $ ./Build reconfig
>> > NOTE: Run ./Build reconfig to change existing configuration.
>> > Reuse previous configuration as defaults? [y ]n
>> >
>> > **Beginning interactive configuration**
>> > Directory for GBrowse's config and support files? [/etc/gbrowse2]
>> > /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
>> > Directory for GBrowse's static images & HTML files?
>> > [/var/www/html/gbrowse2]
>> > /ifs/data/columbia/tm_lab/www/html
>> > Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
>> > Directory for GBrowse's example databases
>> > [/var/www/html/gbrowse2/databases]
>> > /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
>> > Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
>> > /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
>> > Internet port to run demo web site on (for demo)? [8000]
>> > Apache loadable module directory (for demo)? [/etc/httpd/modules]
>> > User account under which Apache daemon runs? [apache] www-data
>> > Automatically update Apache config files to run GBrowse? [y]
>> > Automatically update system config files to run gbrowse-slave? [y]
>> >
>> >
>> > I then run the build which goes smoothly & finally install:
>> > $ ./Build install
>> > NOTE: Run ./Build reconfig to change existing configuration.
>> > Building GBrowse
>> > Files found in blib/arch: installing files in blib/lib into architecture
>> > dependent library tree
>> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> > ERROR: Can't create '/etc/default'
>> > Do not have write permissions on '/etc/default'
>> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> >  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio
>> > XE:
>> > Pinpoint memory and threading errors before they happen.
>> > Find and fix more than 250 security defects in the development cycle.
>> > Locate bottlenecks in serial and parallel code that limit performance.
>> > http://p.sf.net/sfu/intel-dev2devfeb
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
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Re: Gbrowse2.26 non-root install issue

Sean O'Keeffe-2
Todd,
Well done, switching autoconfig off worked.
Thanks a bunch.

Sean.

On 18 February 2011 08:22, Todd Harris <[hidden email]> wrote:
Perhaps try ./Build reconfig and turn off the autoupdate of apache
configuration?

Todd

On Thu, Feb 17, 2011 at 10:31 AM, Sean O'Keeffe <[hidden email]> wrote:
> Sorry for reposting but I'm getting no joy on this:
>
> 1)
> /opt/perl/bin/perl Build.PL --cgibin=/ifs/data/columbia/
> tm_lab/so2346/gbrowse_scripts/cgi-bin
> --conf=/ifs/data/columbia/tm_lab/so2346/gbrowse_scripts/conf
> --htdocs=/ifs/data/columbia/tm_lab/www/html --tmp=/var/tmp/gbrowse2
> --lib=/opt/perl/lib/perl5
>
> 2)
> ./Build install
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ERROR: Can't create '/etc/httpd/conf.d'
> Do not have write permissions on '/etc/httpd/conf.d'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>
> On 16 February 2011 12:56, Scott Cain <[hidden email]> wrote:
>>
>> Hi Sean,
>>
>> Lincoln wrote a few weeks ago about why root is required to install
>> GBrowse even if you are installing into directories that are writeable
>> by your account:
>>
>>
>>  http://gmod.827538.n3.nabble.com/GBrowse-2-23-released-tt2386677.html#a2392535
>>
>> However, that has to do with user accounts and SQLite, whereas the
>> contents of /etc/default is slave renderer info.  I suppose that
>> adding a config option related to that path ought to be added.
>>
>> Scott
>>
>>
>> On Wed, Feb 16, 2011 at 11:58 AM, Sean O'Keeffe <[hidden email]>
>> wrote:
>> > Hi All,
>> > I'm trying to get a local install on a Centos 5 system and I'm getting
>> > an
>> > odd 'can't install into /etc/default' error at Build install stage.
>> > The installed pre-req's are all new as of yesterday incl.
>> > bioperl/biographics etc.
>> > Any help or thoughts would be great.
>> >
>> > Sean.
>> >
>> > My config is as below:
>> >
>> > $ ./Build reconfig
>> > NOTE: Run ./Build reconfig to change existing configuration.
>> > Reuse previous configuration as defaults? [y ]n
>> >
>> > **Beginning interactive configuration**
>> > Directory for GBrowse's config and support files? [/etc/gbrowse2]
>> > /ifs/data/columbia/tm_lab/so2346/gbrowse2/conf
>> > Directory for GBrowse's static images & HTML files?
>> > [/var/www/html/gbrowse2]
>> > /ifs/data/columbia/tm_lab/www/html
>> > Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
>> > Directory for GBrowse's example databases
>> > [/var/www/html/gbrowse2/databases]
>> > /ifs/data/columbia/tm_lab/www/html/gbrowse2/databases
>> > Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
>> > /ifs/data/columbia/tm_lab/so2346/gbrowse2/cgi-bin
>> > Internet port to run demo web site on (for demo)? [8000]
>> > Apache loadable module directory (for demo)? [/etc/httpd/modules]
>> > User account under which Apache daemon runs? [apache] www-data
>> > Automatically update Apache config files to run GBrowse? [y]
>> > Automatically update system config files to run gbrowse-slave? [y]
>> >
>> >
>> > I then run the build which goes smoothly & finally install:
>> > $ ./Build install
>> > NOTE: Run ./Build reconfig to change existing configuration.
>> > Building GBrowse
>> > Files found in blib/arch: installing files in blib/lib into architecture
>> > dependent library tree
>> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> > ERROR: Can't create '/etc/default'
>> > Do not have write permissions on '/etc/default'
>> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> >  at /opt/perl/lib/perl5/Module/Build/Base.pm line 3529
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio
>> > XE:
>> > Pinpoint memory and threading errors before they happen.
>> > Find and fix more than 250 security defects in the development cycle.
>> > Locate bottlenecks in serial and parallel code that limit performance.
>> > http://p.sf.net/sfu/intel-dev2devfeb
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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