[Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

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[Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

Keiran Raine
Hi,

I've installed GBrowse 2.06 as I have previous versions, but I'm finding that it will not pick up any of the contents of the static HTML components and stylesheets.

On investigation in the logs it appears that it is looking in the wrong place:

e.g. [error] [client 172.17.55.2] (13)Permission denied: access to /gbrowse2/js/toggle.js denied, ref

However if you look at the end of the installed ConfigData.pm (prefix is /gbrowse) you can see that htdocs is set as '/gbrowse/var/www/gbrowse2'

do{ my $x = [
       {
         'config_done' => 1,
         'registration_done' => 1,
         'cgibin' => '/gbrowse/usr/lib/cgi-bin/gb2',
         'databases' => '/gbrowse/var/www/gbrowse2/databases',
         'wwwuser' => 'www-data',
         'installconf' => 'n',
         'conf' => '/gbrowse/etc/gbrowse2',
         'htdocs' => '/gbrowse/var/www/gbrowse2',
         'tmp' => '/gbrowse/var/tmp/gbrowse2',
         'portdemo' => 8000,
         'apachemodules' => '/gbrowse/usr/lib/apache2/modules',
         'installetc' => 'n'
       },
       {},
       {}
     ];
$x; }

A fix would be very useful.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100





-- 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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Re: [Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

Keiran Raine
Actually doing some more digging I've realised that this is handled by the apache configuration:

    Alias        "/gbrowse2/i/" "/gbrowse/var/tmp/gbrowse2/images/"
    Alias        "/gbrowse2"    "/gbrowse/var/www/gbrowse2"
    ScriptAlias  "/gb2"      "/gbrowse/usr/lib/cgi-bin/gb2"

But I still can't figure out why it's suddenly stopped working.

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 14 May 2010, at 12:08, Keiran Raine wrote:

Hi,

I've installed GBrowse 2.06 as I have previous versions, but I'm finding that it will not pick up any of the contents of the static HTML components and stylesheets.

On investigation in the logs it appears that it is looking in the wrong place:

e.g. [error] [client 172.17.55.2] (13)Permission denied: access to /gbrowse2/js/toggle.js denied, ref

However if you look at the end of the installed ConfigData.pm (prefix is /gbrowse) you can see that htdocs is set as '/gbrowse/var/www/gbrowse2'

do{ my $x = [
       {
         'config_done' => 1,
         'registration_done' => 1,
         'cgibin' => '/gbrowse/usr/lib/cgi-bin/gb2',
         'databases' => '/gbrowse/var/www/gbrowse2/databases',
         'wwwuser' => 'www-data',
         'installconf' => 'n',
         'conf' => '/gbrowse/etc/gbrowse2',
         'htdocs' => '/gbrowse/var/www/gbrowse2',
         'tmp' => '/gbrowse/var/tmp/gbrowse2',
         'portdemo' => 8000,
         'apachemodules' => '/gbrowse/usr/lib/apache2/modules',
         'installetc' => 'n'
       },
       {},
       {}
     ];
$x; }

A fix would be very useful.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100





-- 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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Re: [Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

Lincoln Stein
In reply to this post by Keiran Raine
It sounds like the Aliases are not going into effect? According to what you sent, /gbrowse2/js/toggle.js should be turned into physical file:

/gbrowse/var/www/gbrowse2/js/toggle.js

Does this file exist on your system, and if so, is it readable by the www-data user? Is the directory path readable  and executable?

Lincoln

On Fri, May 14, 2010 at 7:08 AM, Keiran Raine <[hidden email]> wrote:
Hi,

I've installed GBrowse 2.06 as I have previous versions, but I'm finding that it will not pick up any of the contents of the static HTML components and stylesheets.

On investigation in the logs it appears that it is looking in the wrong place:

e.g. [error] [client 172.17.55.2] (13)Permission denied: access to /gbrowse2/js/toggle.js denied, ref

However if you look at the end of the installed ConfigData.pm (prefix is /gbrowse) you can see that htdocs is set as '/gbrowse/var/www/gbrowse2'

do{ my $x = [
       {
         'config_done' => 1,
         'registration_done' => 1,
         'cgibin' => '/gbrowse/usr/lib/cgi-bin/gb2',
         'databases' => '/gbrowse/var/www/gbrowse2/databases',
         'wwwuser' => 'www-data',
         'installconf' => 'n',
         'conf' => '/gbrowse/etc/gbrowse2',
         'htdocs' => '/gbrowse/var/www/gbrowse2',
         'tmp' => '/gbrowse/var/tmp/gbrowse2',
         'portdemo' => 8000,
         'apachemodules' => '/gbrowse/usr/lib/apache2/modules',
         'installetc' => 'n'
       },
       {},
       {}
     ];
$x; }

A fix would be very useful.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100





-- 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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--
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 <[hidden email]>

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Re: [Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

Keiran Raine
Hi,

The problem was that every time I do a new install to the prefix location it changes the permissions of part of the ../gbrowse2/databases tree so that on the next install it is unable to write to this area, the files end up with ????? permissions (not that I know what this means).

I'd changed the permissions so the install would proceed but the directories were not executable and so the failure.

I'll send a mail if this reoccurs on the next release with full details of the problem files/directories incase this is a problem for all not root users.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 14 May 2010, at 21:54, Lincoln Stein wrote:

It sounds like the Aliases are not going into effect? According to what you sent, /gbrowse2/js/toggle.js should be turned into physical file:

/gbrowse/var/www/gbrowse2/js/toggle.js

Does this file exist on your system, and if so, is it readable by the www-data user? Is the directory path readable  and executable?

Lincoln

On Fri, May 14, 2010 at 7:08 AM, Keiran Raine <[hidden email]> wrote:
Hi,

I've installed GBrowse 2.06 as I have previous versions, but I'm finding that it will not pick up any of the contents of the static HTML components and stylesheets.

On investigation in the logs it appears that it is looking in the wrong place:

e.g. [error] [client 172.17.55.2] (13)Permission denied: access to /gbrowse2/js/toggle.js denied, ref

However if you look at the end of the installed ConfigData.pm (prefix is /gbrowse) you can see that htdocs is set as '/gbrowse/var/www/gbrowse2'

do{ my $x = [
       {
         'config_done' => 1,
         'registration_done' => 1,
         'cgibin' => '/gbrowse/usr/lib/cgi-bin/gb2',
         'databases' => '/gbrowse/var/www/gbrowse2/databases',
         'wwwuser' => 'www-data',
         'installconf' => 'n',
         'conf' => '/gbrowse/etc/gbrowse2',
         'htdocs' => '/gbrowse/var/www/gbrowse2',
         'tmp' => '/gbrowse/var/tmp/gbrowse2',
         'portdemo' => 8000,
         'apachemodules' => '/gbrowse/usr/lib/apache2/modules',
         'installetc' => 'n'
       },
       {},
       {}
     ];
$x; }

A fix would be very useful.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100





-- 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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--
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 <[hidden email]>


-- 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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Re: [Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

Lincoln Stein
If reproducible, this is a pretty major bug in the installer. Is it just growse2/databases, or are other trees affected as well? The js directory is not part of the subtree, so I don't know why you were getting a permission denied on javascript and css files.

If possible, could you send me a recursive long directory listing of /gbrowse/var/www/gbrowse2/databases and /gbrowse/var/www/gbrowse2 after a fresh, bad install so that I can try to figure out what's going wrong? Obviously this isn't happening to me.

????? permissions is a bit weird. Are you installing on an NFS server by any chance?

Lincoln

On Fri, May 14, 2010 at 5:34 PM, Keiran Raine <[hidden email]> wrote:
Hi,

The problem was that every time I do a new install to the prefix location it changes the permissions of part of the ../gbrowse2/databases tree so that on the next install it is unable to write to this area, the files end up with ????? permissions (not that I know what this means).

I'd changed the permissions so the install would proceed but the directories were not executable and so the failure.

I'll send a mail if this reoccurs on the next release with full details of the problem files/directories incase this is a problem for all not root users.

Regards,


Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 14 May 2010, at 21:54, Lincoln Stein wrote:

It sounds like the Aliases are not going into effect? According to what you sent, /gbrowse2/js/toggle.js should be turned into physical file:

/gbrowse/var/www/gbrowse2/js/toggle.js

Does this file exist on your system, and if so, is it readable by the www-data user? Is the directory path readable  and executable?

Lincoln

On Fri, May 14, 2010 at 7:08 AM, Keiran Raine <[hidden email]> wrote:
Hi,

I've installed GBrowse 2.06 as I have previous versions, but I'm finding that it will not pick up any of the contents of the static HTML components and stylesheets.

On investigation in the logs it appears that it is looking in the wrong place:

e.g. [error] [client 172.17.55.2] (13)Permission denied: access to /gbrowse2/js/toggle.js denied, ref

However if you look at the end of the installed ConfigData.pm (prefix is /gbrowse) you can see that htdocs is set as '/gbrowse/var/www/gbrowse2'

do{ my $x = [
       {
         'config_done' => 1,
         'registration_done' => 1,
         'cgibin' => '/gbrowse/usr/lib/cgi-bin/gb2',
         'databases' => '/gbrowse/var/www/gbrowse2/databases',
         'wwwuser' => 'www-data',
         'installconf' => 'n',
         'conf' => '/gbrowse/etc/gbrowse2',
         'htdocs' => '/gbrowse/var/www/gbrowse2',
         'tmp' => '/gbrowse/var/tmp/gbrowse2',
         'portdemo' => 8000,
         'apachemodules' => '/gbrowse/usr/lib/apache2/modules',
         'installetc' => 'n'
       },
       {},
       {}
     ];
$x; }

A fix would be very useful.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100





-- 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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--
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 <[hidden email]>


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



--
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 <[hidden email]>

------------------------------------------------------------------------------


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Re: [Gmod-gbrowse] Problems with 2.06 when using 'Build.PL --prefix'

Keiran Raine
Ok,

So the problem is partially the installer and partially me (no surprise there).

If you try to install over the top of an existing one the install fails if you are non-root as the permissions of several files in the databases area are read-only.

The executable directory was due to me doing a recursive chmod on '/gbrowse/var/www/' and not allowing executable on the directories.

Hope this is more useful.

Regards,

cgp-gbrowse[kr2]34: ll -r /gbrowse/var/www/gbrowse2/databases/*
/gbrowse/var/www/gbrowse2/databases/yeast_scaffolds:
total 1.1M
-r--r--r-- 1 kr2 team78  192 2010-05-14 11:51 chromosomes.gff3
-r--r--r-- 1 kr2 team78 808K 2010-05-14 11:51 chr2.fa
-r--r--r-- 1 kr2 team78 229K 2010-05-14 11:51 chr1.fa

/gbrowse/var/www/gbrowse2/databases/yeast_chr1+2:
total 312K
-r--r--r-- 1 kr2 team78 305K 2010-05-14 11:51 yeast_chr1+2.gff3

/gbrowse/var/www/gbrowse2/databases/pop_demo:
total 4.0K
-r--r--r-- 1 kr2 team78 490 2010-05-14 11:51 pop_demo.gff3

/gbrowse/var/www/gbrowse2/databases/ideograms:
total 152K
-r--r--r-- 1 kr2 team78 23K 2010-05-14 11:51 rat_cytobands.gff
-r--r--r-- 1 kr2 team78 38K 2010-05-14 11:51 mouse_cytobands.gff
-r--r--r-- 1 kr2 team78 81K 2010-05-14 11:51 human_cytobands.gff

/gbrowse/var/www/gbrowse2/databases/gbrowse_syn:
total 12K
drwxr-xr-x 2 kr2 team78 4.0K 2010-05-14 22:47 wild_rice/
drwxr-xr-x 2 kr2 team78 4.0K 2010-05-14 22:47 rice/
drwxr-xr-x 2 kr2 team78 4.0K 2010-05-14 22:47 alignments/

/gbrowse/var/www/gbrowse2/databases/admin_uploads:
total 4.0K
-r--r--r-- 1 kr2 team78 144 2010-05-14 11:51 README


Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 14 May 2010, at 22:43, Lincoln Stein wrote:

If reproducible, this is a pretty major bug in the installer. Is it just growse2/databases, or are other trees affected as well? The js directory is not part of the subtree, so I don't know why you were getting a permission denied on javascript and css files.

If possible, could you send me a recursive long directory listing of /gbrowse/var/www/gbrowse2/databases and /gbrowse/var/www/gbrowse2 after a fresh, bad install so that I can try to figure out what's going wrong? Obviously this isn't happening to me.

????? permissions is a bit weird. Are you installing on an NFS server by any chance?

Lincoln

On Fri, May 14, 2010 at 5:34 PM, Keiran Raine <[hidden email]> wrote:
Hi,

The problem was that every time I do a new install to the prefix location it changes the permissions of part of the ../gbrowse2/databases tree so that on the next install it is unable to write to this area, the files end up with ????? permissions (not that I know what this means).

I'd changed the permissions so the install would proceed but the directories were not executable and so the failure.

I'll send a mail if this reoccurs on the next release with full details of the problem files/directories incase this is a problem for all not root users.

Regards,


Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 14 May 2010, at 21:54, Lincoln Stein wrote:

It sounds like the Aliases are not going into effect? According to what you sent, /gbrowse2/js/toggle.js should be turned into physical file:

/gbrowse/var/www/gbrowse2/js/toggle.js

Does this file exist on your system, and if so, is it readable by the www-data user? Is the directory path readable  and executable?

Lincoln

On Fri, May 14, 2010 at 7:08 AM, Keiran Raine <[hidden email]> wrote:
Hi,

I've installed GBrowse 2.06 as I have previous versions, but I'm finding that it will not pick up any of the contents of the static HTML components and stylesheets.

On investigation in the logs it appears that it is looking in the wrong place:

e.g. [error] [client 172.17.55.2] (13)Permission denied: access to /gbrowse2/js/toggle.js denied, ref

However if you look at the end of the installed ConfigData.pm (prefix is /gbrowse) you can see that htdocs is set as '/gbrowse/var/www/gbrowse2'

do{ my $x = [
       {
         'config_done' => 1,
         'registration_done' => 1,
         'cgibin' => '/gbrowse/usr/lib/cgi-bin/gb2',
         'databases' => '/gbrowse/var/www/gbrowse2/databases',
         'wwwuser' => 'www-data',
         'installconf' => 'n',
         'conf' => '/gbrowse/etc/gbrowse2',
         'htdocs' => '/gbrowse/var/www/gbrowse2',
         'tmp' => '/gbrowse/var/tmp/gbrowse2',
         'portdemo' => 8000,
         'apachemodules' => '/gbrowse/usr/lib/apache2/modules',
         'installetc' => 'n'
       },
       {},
       {}
     ];
$x; }

A fix would be very useful.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100





-- 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.

------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
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 <[hidden email]>


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



--
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 <[hidden email]>


-- 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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