there are no "GC content and 6 frame translation" data displayed when done by tutorial

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there are no "GC content and 6 frame translation" data displayed when done by tutorial

EmanLee
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
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security issues and trends.  Skip the complicated setup - simply import
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

Scott Cain
Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
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security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

EmanLee
Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
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



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

Keiran Raine
Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
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


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- 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.

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

EmanLee
Hi Keiran,
Thanks. I un-checked "Cache tracks", restarted apache server, used another web browser(Google Chrome), changed the region for search.
But, GC  content  and 6-frame did not appear.
<img src="http://gmod.827538.n3.nabble.com/attachment/4040167/0/screen_shot_gbrowse_no_GC_content_6_frame.jpg" onload="parent.parent.MM.compose.setPic(this);parent.parent.fClearMsg();this.onload=null;" border="0">

--
Thanks
Eman

在2014-01-29,"Keiran Raine" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Keiran Raine" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



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


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
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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 company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



------------------------------------------------------------------------------
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security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

EmanLee
Hi, All
We installed GBrowse 2.55 on another computer named PC001(same environments as the previous computer), and GBrowse on PC001 works.
On previous computer, some recommended packages were not installed.
On PC001, we installed all packages (including essential and recommended packages), especially all those related to Graphics.

Thanks
Eman

在2014-01-29,"EmanLee" <[hidden email]> 写道:
-----原始邮件-----
发件人:"EmanLee" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"Keiran Raine" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Keiran,
Thanks. I un-checked "Cache tracks", restarted apache server, used another web browser(Google Chrome), changed the region for search.
But, GC  content  and 6-frame did not appear.


--
Thanks
Eman

在2014-01-29,"Keiran Raine" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Keiran Raine" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
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


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- 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.





------------------------------------------------------------------------------
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

Scott Cain
Hi Eman,

Do you have any idea what packages where missing from the first server?  Certainly, this should work with only the required packages.

Scott



On Tue, Feb 18, 2014 at 10:40 PM, EmanLee <[hidden email]> wrote:
Hi, All
We installed GBrowse 2.55 on another computer named PC001(same environments as the previous computer), and GBrowse on PC001 works.
On previous computer, some recommended packages were not installed.
On PC001, we installed all packages (including essential and recommended packages), especially all those related to Graphics.

Thanks
Eman

在2014-01-29,"EmanLee" <[hidden email]> 写道:
-----原始邮件-----
发件人:"EmanLee" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"Keiran Raine" <[hidden email]>

抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial


Hi Keiran,
Thanks. I un-checked "Cache tracks", restarted apache server, used another web browser(Google Chrome), changed the region for search.
But, GC  content  and 6-frame did not appear.


--
Thanks
Eman

在2014-01-29,"Keiran Raine" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Keiran Raine" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- 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.







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

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

EmanLee
Hi, Scott
I compared both install log files.  Only GraphViz was not installed on previous computer.
I attached the log files for your reference.

--
Thanks
Eman

在2014-02-20,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年02月20日 星期四
收件人:"EmanLee" <[hidden email]>
抄送:"Keiran Raine" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Do you have any idea what packages where missing from the first server?  Certainly, this should work with only the required packages.

Scott



On Tue, Feb 18, 2014 at 10:40 PM, EmanLee <[hidden email]> wrote:
Hi, All
We installed GBrowse 2.55 on another computer named PC001(same environments as the previous computer), and GBrowse on PC001 works.
On previous computer, some recommended packages were not installed.
On PC001, we installed all packages (including essential and recommended packages), especially all those related to Graphics.

Thanks
Eman

在2014-01-29,"EmanLee" <[hidden email]> 写道:
-----原始邮件-----
发件人:"EmanLee" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"Keiran Raine" <[hidden email]>

抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial


Hi Keiran,
Thanks. I un-checked "Cache tracks", restarted apache server, used another web browser(Google Chrome), changed the region for search.
But, GC  content  and 6-frame did not appear.


--
Thanks
Eman

在2014-01-29,"Keiran Raine" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Keiran Raine" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- 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.







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



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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

Scott Cain
I guarantee graphviz had nothing to do with this problem. GBrowse doesn't use graphviz for anything

Scott


Sent from my iPhone

On Feb 25, 2014, at 4:10 PM, EmanLee <[hidden email]> wrote:

Hi, Scott
I compared both install log files.  Only GraphViz was not installed on previous computer.
I attached the log files for your reference.

--
Thanks
Eman

在2014-02-20,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年02月20日 星期四
收件人:"EmanLee" <[hidden email]>
抄送:"Keiran Raine" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Do you have any idea what packages where missing from the first server?  Certainly, this should work with only the required packages.

Scott



On Tue, Feb 18, 2014 at 10:40 PM, EmanLee <[hidden email]> wrote:
Hi, All
We installed GBrowse 2.55 on another computer named PC001(same environments as the previous computer), and GBrowse on PC001 works.
On previous computer, some recommended packages were not installed.
On PC001, we installed all packages (including essential and recommended packages), especially all those related to Graphics.

Thanks
Eman

在2014-01-29,"EmanLee" <[hidden email]> 写道:
-----原始邮件-----
发件人:"EmanLee" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"Keiran Raine" <[hidden email]>

抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial


Hi Keiran,
Thanks. I un-checked "Cache tracks", restarted apache server, used another web browser(Google Chrome), changed the region for search.
But, GC  content  and 6-frame did not appear.


--
Thanks
Eman

在2014-01-29,"Keiran Raine" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Keiran Raine" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- 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.







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


<gbrowse_install_logs_on_PC001.sh>
<gbrowse_install_logs_on_previous_pc.sh>

------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
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Re: there are no "GC content and 6 frame translation" data displayed when done by tutorial

EmanLee
Hi, Scott

I re-installed the following packages and "GC content" worked well:
sudo perl -MCPAN -e'install GraphViz'
sudo perl -MCPAN -e'install Bio::Root::Version'
sudo perl -MCPAN -e'install Bio::Perl'

--
Thanks
Eman

在2014-02-25,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年02月25日 星期二
收件人:"EmanLee" <[hidden email]>
抄送:"Keiran Raine" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

I guarantee graphviz had nothing to do with this problem. GBrowse doesn't use graphviz for anything

Scott


Sent from my iPhone

On Feb 25, 2014, at 4:10 PM, EmanLee <[hidden email]> wrote:

Hi, Scott
I compared both install log files.  Only GraphViz was not installed on previous computer.
I attached the log files for your reference.

--
Thanks
Eman

在2014-02-20,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年02月20日 星期四
收件人:"EmanLee" <[hidden email]>
抄送:"Keiran Raine" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Do you have any idea what packages where missing from the first server?  Certainly, this should work with only the required packages.

Scott



On Tue, Feb 18, 2014 at 10:40 PM, EmanLee <[hidden email]> wrote:
Hi, All
We installed GBrowse 2.55 on another computer named PC001(same environments as the previous computer), and GBrowse on PC001 works.
On previous computer, some recommended packages were not installed.
On PC001, we installed all packages (including essential and recommended packages), especially all those related to Graphics.

Thanks
Eman

在2014-01-29,"EmanLee" <[hidden email]> 写道:
-----原始邮件-----
发件人:"EmanLee" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"Keiran Raine" <[hidden email]>

抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial


Hi Keiran,
Thanks. I un-checked "Cache tracks", restarted apache server, used another web browser(Google Chrome), changed the region for search.
But, GC  content  and 6-frame did not appear.


--
Thanks
Eman

在2014-01-29,"Keiran Raine" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Keiran Raine" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"Scott Cain" <[hidden email]>;"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

Are you viewing exactly the same region you did before deletion of the 'directory.index'?  If so the image may be cached, I don't think it checks for changes if it can find a cached image.  To force it go to the interface and select the 'Preferences' tab, de-select 'Cache tracks' and hit 'Update Appearance'.



Kind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 29 Jan 2014, at 03:39, EmanLee <[hidden email]> wrote:

Hi Scott,
Thanks your advice. We removed directory.index and then visited that page, it's still blank.
And, there were no errors output to the apache log file. Steps were listed below:

[root@testtest volvox]# pwd
/var/lib/gbrowse2/databases/volvox
[root@testtest volvox]# rm -rf directory.index
[root@testtest volvox]# ll
total 128
-rw-r--r-- 1 root root 28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root root   221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root root  1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root root   730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root root 50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root root   405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root root   722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root root  9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root root   122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root root   906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root root    88 Jan 24 16:33 volvox_trace.gff3
visited that page(/cgi-bin/gb2/gbrowse/volvox/), they(DNA,frame) are still blank.
[root@testtest volvox]# ll
total 136
-rw-r--r-- 1 apache apache 12288 Jan 29 11:15 directory.index
-rw-r--r-- 1 root   root   28797 Jan 24 16:33 volvox_array.gff3
-rw-r--r-- 1 root   root     221 Jan 24 16:33 volvox_bacs.gff3
-rw-r--r-- 1 root   root    1170 Jan 24 16:33 volvox_domains.gff3
-rw-r--r-- 1 root   root     730 Jan 24 16:33 volvox_est.gff3
-rw-r--r-- 1 root   root   50841 Jan 24 16:33 volvox.fa
-rw-r--r-- 1 root   root     405 Jan 24 16:33 volvox_geneproducts.gff3
-rw-r--r-- 1 root   root     722 Jan 24 16:33 volvox_genes_simple.gff3
-rw-r--r-- 1 root   root    9583 Jan 24 16:33 volvox_matches.gff3
-rw-r--r-- 1 root   root     122 Jan 24 16:33 volvox_microarray.gff3
-rw-r--r-- 1 root   root     906 Jan 24 16:33 volvox_remarks.gff3
-rw-r--r-- 1 root   root      88 Jan 24 16:33 volvox_trace.gff3
checked the apache log file, no errors.

--
Thanks
Eman

在2014-01-29,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年01月29日 星期三
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] there are no "GC content and 6 frame translation" data displayed when done by tutorial

Hi Eman,

The most likely problem is that you tried to view the DNA and GC content before you added the fasta file.  When that happens, GBrowse will create the directory.index file with nothing in it.  GBrowse doesn't know that you added a fasta file after that, so it continues to think there is nothing there.  The fix is to delete the directory.index file and try again.

Scott



On Mon, Jan 27, 2014 at 7:36 AM, EmanLee <[hidden email]> wrote:
I have followed all the steps (include the GC content and 6 frame translation) in the gbrowse 2.55 tutorial.html (on CentoOS 6.4 x86_64).
But, there are no "GC content and 6 frame translation" data displayed as the snapscreen image.


We checked the following files:
(1)
apache error logs:
MSG: Got a sequence without letters. Could not guess alphabet, referer: http://202.200.111.222/cgi-bin/gb2/gbrowse/volvox/

(2)
ll /var/lib/gbrowse2/databases/
drwxrwxrwx  2 root   root    4096 Jan 27 17:49 volvox

ll /var/lib/gbrowse2/databases/volvox
-rw-r--r-- 1 apache apache 12288 Jan 27 17:49 directory.index

wc directory.index
    0     3 12288 directory.index

(3)
We have put several volvox*.gff3(including volvox_remarks.gff3) files into /var/lib/gbrowse2/databases/volvox/

(4)
we have put volvox.fa into /var/lib/gbrowse2/databases/volvox/
more /var/lib/gbrowse2/databases/volvox/volvox.fa
>ctgA
cattgttgcggagttgaacaacggcattaggaacacttccgtctctcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
......

(5)
volvox.conf in /etc/gbrowse2

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/var/lib/gbrowse2/databases/volvox'
......
[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
key            = DNA/GC Content
......

Thanks.
eman



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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- 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.







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


<gbrowse_install_logs_on_PC001.sh>
<gbrowse_install_logs_on_previous_pc.sh>



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