GBrowse VM's

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GBrowse VM's

Jacqueline Lee

Hi Scott,

 

I’m not a systems person and our sysadmin is not in today, so please forgive me if this is a silly question. Our new installation of GBrowse is not working and it looks like it will take me a while to figure out exactly what is going on. We have a conference coming up in 9 days at which we need to display some BAM files on our GBrowse. Our old GBrowse is on a very old machine that is desperately in need of patching and is getting errors when I attempt to build Bio::DB::Sam on it.  I very much doubt I will be able to display the BAM files on either machine by the time the conference happens. I will keep trying and I’ll e-mail the gbrowse mailing list just in case someone can help with the errors installing Bio::DB::Sam.

 

We are running VMWare on our new servers and I noticed you provide .ova VMs that have a working GBrowse. I’m not sure what security risks or other issues might be involved in using one of these machines (even temporarily) in place of our current GBrowse VM, but I thought I would ask, just in case it can be done.

 

Thanks,

 

Jacqueline Lee

Xenbase Bioinformatician/ Software Developer

e-mail: [hidden email]

www.xenbase.org

 


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Re: GBrowse VM's

Kandalaft, Iyad
Hi Jacqueline

The VM is only as secure as the administrator makes it out to be.  Also, your security considerations would have to take into account whether this is for external or internal use or both.  External use has many other security considerations that need to be addressed and I wouldn't simply take a VM and launch it on my network.  For internal use, the VM wouldn't be a big deal.

Are you using the cpan module to install the DB::Sam module?  If so, what errors does it produce?  Typically, it complains because there are dependencies that haven't been install yet, which means you'll have to install those first.  If it's giving some other error where it's using native system libraries, then you would need to install those first.  I copied the first line from the CPAN.org side " This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases."  This means you need to install libbam.  On debian linux "sudo apt-get install libbam-dev" or red hat linux "sudo yum install libbam-dev" (I'm not sure about the redhat library name).


Iyad Kandalaft
Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.
[hidden email]
613-759-1228
Government of Canada | Gouvernement du Canada



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To: [hidden email]
Subject: Gmod-gbrowse Digest, Vol 87, Issue 6



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Today's Topics:

   1. GBrowse VM's (Jacqueline Lee)
   2. Bio::DB::Sam issues (Jacqueline Lee)
   3. Re: Bio::DB::Sam issues (Jacqueline Lee)
   4. Bug? Balloon hover callback being called with 2 different
      objects (Keiran Raine)
   5. balloon hover, can I turn it off in a semantic zoom?
      (Keiran Raine)
   6. Broken links on
      http://gmod.org/gbrowse2/tutorial/tutorial.html (Nic Herndon)
   7. GMOD grant application letter of support (Scott Cain)
   8. getting balloon click to use the URL generated by 'link =
      AUTO' (Keiran Raine)


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

Message: 1
Date: Wed, 14 Aug 2013 09:30:44 -0600
From: Jacqueline Lee <[hidden email]>
Subject: [Gmod-gbrowse] GBrowse VM's
To: "'[hidden email]'" <[hidden email]>
Cc: "'[hidden email]'"
        <[hidden email]>
Message-ID:
        <[hidden email]>
       
Content-Type: text/plain; charset="us-ascii"

Hi Scott,

I'm not a systems person and our sysadmin is not in today, so please forgive me if this is a silly question. Our new installation of GBrowse is not working and it looks like it will take me a while to figure out exactly what is going on. We have a conference coming up in 9 days at which we need to display some BAM files on our GBrowse. Our old GBrowse is on a very old machine that is desperately in need of patching and is getting errors when I attempt to build Bio::DB::Sam on it.  I very much doubt I will be able to display the BAM files on either machine by the time the conference happens. I will keep trying and I'll e-mail the gbrowse mailing list just in case someone can help with the errors installing Bio::DB::Sam.

We are running VMWare on our new servers and I noticed you provide .ova VMs that have a working GBrowse. I'm not sure what security risks or other issues might be involved in using one of these machines (even temporarily) in place of our current GBrowse VM, but I thought I would ask, just in case it can be done.

Thanks,

Jacqueline Lee
Xenbase Bioinformatician/ Software Developer
e-mail: [hidden email]<mailto:[hidden email]>
www.xenbase.org

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Message: 2
Date: Wed, 14 Aug 2013 10:10:36 -0600
From: Jacqueline Lee <[hidden email]>
Subject: [Gmod-gbrowse] Bio::DB::Sam issues
To: "'[hidden email]'"
        <[hidden email]>
Message-ID:
        <[hidden email]>
       
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I've tried to build and install Bio::DB::Sam on two different GBrowse servers. I can run Build.PL, but when I actually try to run ./Build I get the following error:

/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

I'm not sure at all what could be causing this. I am using samtools 0.1.18 and it installed correctly.

The entire output is below:

Building Bio-SamTools
gcc -I/usr/local/src/samtools-0.1.18 -Ic_bin -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.38" -DVERSION="1.38" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_open?:
lib/Bio/DB/Sam.c:547: warning: unused variable ?packname?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_index_build?:
lib/Bio/DB/Sam.c:605: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_sort_core?:
lib/Bio/DB/Sam.xs:322: warning: implicit declaration of function ?bam_sort_core?
lib/Bio/DB/Sam.c:629: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_tell?:
lib/Bio/DB/Sam.xs:364: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:366: warning: format ?%llu? expects type ?long long unsigned int?, but argument 5 has type ?int64_t?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_qseq?:
lib/Bio/DB/Sam.xs:516: warning: operation on ?seq? may be undefined
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment__qscore?:
lib/Bio/DB/Sam.xs:530: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux?:
lib/Bio/DB/Sam.xs:589: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__builtin___strncat_chk? differ in signedness
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__strncat_ichk? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux_keys?:
lib/Bio/DB/Sam.xs:685: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_data?:
lib/Bio/DB/Sam.xs:708: warning: pointer targets in assignment differ in signedness
lib/Bio/DB/Sam.xs:711: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Header_view1?:
lib/Bio/DB/Sam.xs:914: warning: implicit declaration of function ?bam_view1?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam__Index_coverage?:
lib/Bio/DB/Sam.xs:999: warning: unused variable ?cov?
lib/Bio/DB/Sam.c: In function ?invoke_pileup_callback_fun?:
lib/Bio/DB/Sam.xs:149: warning: control reaches end of non-void function
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/local/src/samtools-0.1.18 -lbam -lpthread -lz
/usr/bin/ld: /usr/local/src/samtools-0.1.18/libbam.a(bgzf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

If anyone has an idea of how to fix this, it would be appreciated.

Thank you,
Jacqueline Lee
Xenbase Bioinformatician/ Software Developer
e-mail: [hidden email]<mailto:[hidden email]>
www.xenbase.org

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Message: 3
Date: Wed, 14 Aug 2013 10:21:20 -0600
From: Jacqueline Lee <[hidden email]>
Subject: Re: [Gmod-gbrowse] Bio::DB::Sam issues
To: "'[hidden email]'"
        <[hidden email]>
Message-ID:
        <[hidden email]>
       
Content-Type: text/plain; charset="iso-8859-1"

Hello,

Almost immediately after I sent this, I found the solution at http://www.linuxquestions.org/questions/linux-software-2/failed-to-install-sam-pm-884016/.

I hadn't compiled my libbam.a with -fPIC, so I needed to add the flag to my Makefile in my $SAMTOOLS directory.

Jacqueline

From: Jacqueline Lee
Sent: Wednesday, August 14, 2013 10:11 AM
To: '[hidden email]'
Subject: Bio::DB::Sam issues

Hello,

I've tried to build and install Bio::DB::Sam on two different GBrowse servers. I can run Build.PL, but when I actually try to run ./Build I get the following error:

/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

I'm not sure at all what could be causing this. I am using samtools 0.1.18 and it installed correctly.

The entire output is below:

Building Bio-SamTools
gcc -I/usr/local/src/samtools-0.1.18 -Ic_bin -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.38" -DVERSION="1.38" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_open?:
lib/Bio/DB/Sam.c:547: warning: unused variable ?packname?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_index_build?:
lib/Bio/DB/Sam.c:605: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_sort_core?:
lib/Bio/DB/Sam.xs:322: warning: implicit declaration of function ?bam_sort_core?
lib/Bio/DB/Sam.c:629: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_tell?:
lib/Bio/DB/Sam.xs:364: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:366: warning: format ?%llu? expects type ?long long unsigned int?, but argument 5 has type ?int64_t?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_qseq?:
lib/Bio/DB/Sam.xs:516: warning: operation on ?seq? may be undefined
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment__qscore?:
lib/Bio/DB/Sam.xs:530: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux?:
lib/Bio/DB/Sam.xs:589: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__builtin___strncat_chk? differ in signedness
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__strncat_ichk? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux_keys?:
lib/Bio/DB/Sam.xs:685: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_data?:
lib/Bio/DB/Sam.xs:708: warning: pointer targets in assignment differ in signedness
lib/Bio/DB/Sam.xs:711: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Header_view1?:
lib/Bio/DB/Sam.xs:914: warning: implicit declaration of function ?bam_view1?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam__Index_coverage?:
lib/Bio/DB/Sam.xs:999: warning: unused variable ?cov?
lib/Bio/DB/Sam.c: In function ?invoke_pileup_callback_fun?:
lib/Bio/DB/Sam.xs:149: warning: control reaches end of non-void function
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/local/src/samtools-0.1.18 -lbam -lpthread -lz
/usr/bin/ld: /usr/local/src/samtools-0.1.18/libbam.a(bgzf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

If anyone has an idea of how to fix this, it would be appreciated.

Thank you,
Jacqueline Lee
Xenbase Bioinformatician/ Software Developer
e-mail: [hidden email]<mailto:[hidden email]>
www.xenbase.org<http://www.xenbase.org>

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Message: 4
Date: Thu, 15 Aug 2013 10:20:22 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] Bug? Balloon hover callback being called with
        2 different objects
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I'm currently building a new GBrowse instance with v2.55 and after copying across our old callback module I've found that I'm getting odd errors when call-backs are run on BAM track elements like:

An error occurred while evaluating the callback at section='812_PD4107a_bwa', option='balloon hover':
   => Can't locate object method "flag" via package "Bio::SeqFeature::Lite"

I did some digging and the problem that appears to be occurring is that the call back is being called twice once with the expected BAM object:

        Bio::DB::Bam::AlignWrapper

and then again with the unexpected:

        Bio::SeqFeature::Lite

I've prevented the spamming of my error logs by adding the following to the beginning of my call back:

        return unless($f->can('flag'));

I'm guessing that this is creating additional unnecessary load on the server so probably worth investigating.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

[hidden email]
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104




--
 The Wellcome Trust Sanger Institute is operated by Genome Rese arch  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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Message: 5
Date: Thu, 15 Aug 2013 10:34:34 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] balloon hover, can I turn it off in a semantic
        zoom?
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I have a BAM track configured with semantic zoom.

>From 1-150 bp I have a detailed popup of the read details and above that I want the balloons to not be rendered, e.g.:

[562_TR-1_RNA_ribozero_bwa]
...
balloon hover   = sub {&Sanger::CGP::GBrowse::GB_Init_Code::bam_tooltip(shift)}

[562_TR-1_RNA_ribozero_bwa:150]
balloon hover = 0

The problem I have is that even when 'ballon hover' is set to false a default ballonis generated (see attached).  Ideally I want to reduce the data being served and completely disable this behaviour at this zoom level.  I'm aware that this can be switched to a standard 'title' mouse over by changing 'titles are balloons', but I actually want the image map to be as minimal as possible.

Is it possible to completely turn off this feature?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

[hidden email]
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104




--
 The Wellcome Trust Sanger Institute is operated by Genome Rese arch  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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Message: 6
Date: Wed, 14 Aug 2013 16:45:56 -0400 (EDT)
From: Nic Herndon <[hidden email]>
Subject: [Gmod-gbrowse] Broken links on
        http://gmod.org/gbrowse2/tutorial/tutorial.html
To: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

The Generic Genome Browser Version 2: A Tutorial for Administrators at http://gmod.org/gbrowse2/tutorial/tutorial.html mentions a couple of directories that cannot be accessed: data_files (http://gmod.org/gbrowse2/tutorial/data_files/) and conf_files (http://gmod.org/gbrowse2/tutorial/conf_files/). When trying to access them the server returns the following error message.



Forbidden


You don't have permission to access /gbrowse2/tutorial/data_files/ on this server.


Apache/2.2.9 (Debian) PHP/5.2.6-1+lenny16 with Suhosin-Patch mod_ssl/2.2.9 OpenSSL/0.9.8g Server at gmod.org Port 80
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Message: 7
Date: Mon, 19 Aug 2013 15:01:00 -0400
From: Scott Cain <[hidden email]>
Subject: [Gmod-gbrowse] GMOD grant application letter of support
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="windows-1252"

 Hi all,

First, if you've already received this request, please accept my apologies; as you might imagine, I'm trying to blanket the world a few times over :-) I'm also working through the list of ?known? users of GMOD software, so you may get it again in the near future.

As you may have heard, we (Lincoln Stein, Ian Holmes and I) are applying for a grant to continue work on aspects of the GMOD project, particularly JBrowse and Chado development and GMOD coordination (standards, meetings and courses). We are applying for a community resources for genomics grant from the NIH:

http://grants.nih.gov/grants/guide/pa-files/PAR-11-095.html

for which we think GMOD is an excellent fit. One of the things we need to demonstrate for this grant is that we in fact support the community and have the support of the community, and one way we'd like to show that is with many letters of support. Would you be willing to write such a letter?
It could include information about how you've used or are planning to use GMOD software. To help you get started, I wrote some template paragraphs:

http://gmod.org/wiki/User:Scott#Support_letter_templates

The letters should be on institutional letterhead, signed and then scanned to a PDF or you could mail the original to me and I'll scan them.

The deadline for getting the letters of support back to me is September 3.
Please let me know if you're willing to write one and if there is anything I can do to help you.

Thanks so much,
Scott

--
------------------------------------------------------------------------
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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Message: 8
Date: Wed, 21 Aug 2013 12:49:51 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] getting balloon click to use the URL generated
        by 'link = AUTO'
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I'm trying to get balloon click to use the URL generated by the AUTO option that can be applied to the link option.

I could construct the URL but I can't figure out where I would get the datasource component of the URL:

e.g. 'link = AUTO' generates this:

http://.../gbrowse_details/PD10021_37_58?ref=12;start=25358182;end=25403854;name=KRAS;class=Sequence;feature_id=242107;db_id=REFSEQ%3Adatabase

And I can construct the following which gives the same page, but how can I determine the source (in red)?

balloon click = http://.../gbrowse_details/PD10021_37_58?name=$name;feature_id=$id;db_id=REFSEQ%3Adatabase

or

balloon click = url:../../gbrowse_details/PD10021_37_58?name=$name;feature_id=$id;db_id=REFSEQ%3Adatabase

Am I going about this the wrong way?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

[hidden email]
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104




--
 The Wellcome Trust Sanger Institute is operated by Genome Rese arch  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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Re: GBrowse VM's

Lincoln Stein
Hi,

I'm just back from vacation and I'm unclear whether I'm seeing the whole thread of emails on this subject. 

With regard to the VM, it's a pretty secure machine if you do two things before connecting it to the Internet:
  • Change the "admin" password.
  • Use the built-in "Update Manager" to update the system software to obtain the latest security patches.
With regards to being unable to compile Bio::DB::SAM, this is a FAQ described in the Bio-Samtools README. You will need to go back to the samtools directory, add the -fPIC option to CFLAGS (as described in the README), and recompile the libbam.a library file. After this, Bio::DB::SAM should compile and link fine.

Lincoln



On Wed, Aug 21, 2013 at 9:18 AM, Kandalaft, Iyad <[hidden email]> wrote:
Hi Jacqueline

The VM is only as secure as the administrator makes it out to be.  Also, your security considerations would have to take into account whether this is for external or internal use or both.  External use has many other security considerations that need to be addressed and I wouldn't simply take a VM and launch it on my network.  For internal use, the VM wouldn't be a big deal.

Are you using the cpan module to install the DB::Sam module?  If so, what errors does it produce?  Typically, it complains because there are dependencies that haven't been install yet, which means you'll have to install those first.  If it's giving some other error where it's using native system libraries, then you would need to install those first.  I copied the first line from the CPAN.org side " This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases."  This means you need to install libbam.  On debian linux "sudo apt-get install libbam-dev" or red hat linux "sudo yum install libbam-dev" (I'm not sure about the redhat library name).


Iyad Kandalaft
Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.
[hidden email]
<a href="tel:613-759-1228" value="+16137591228">613-759-1228
Government of Canada | Gouvernement du Canada



-----Original Message-----
From: [hidden email] [mailto:[hidden email]]
Sent: Wednesday, August 21, 2013 7:50 AM
To: [hidden email]
Subject: Gmod-gbrowse Digest, Vol 87, Issue 6



Send Gmod-gbrowse mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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Today's Topics:

   1. GBrowse VM's (Jacqueline Lee)
   2. Bio::DB::Sam issues (Jacqueline Lee)
   3. Re: Bio::DB::Sam issues (Jacqueline Lee)
   4. Bug? Balloon hover callback being called with 2   different
      objects (Keiran Raine)
   5. balloon hover, can I turn it off in a semantic zoom?
      (Keiran Raine)
   6. Broken links on
      http://gmod.org/gbrowse2/tutorial/tutorial.html (Nic Herndon)
   7. GMOD grant application letter of support (Scott Cain)
   8. getting balloon click to use the URL generated by 'link =
      AUTO' (Keiran Raine)


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

Message: 1
Date: Wed, 14 Aug 2013 09:30:44 -0600
From: Jacqueline Lee <[hidden email]>
Subject: [Gmod-gbrowse] GBrowse VM's
To: "'[hidden email]'" <[hidden email]>
Cc: "'[hidden email]'"
        <[hidden email]>
Message-ID:
        <[hidden email]>

Content-Type: text/plain; charset="us-ascii"

Hi Scott,

I'm not a systems person and our sysadmin is not in today, so please forgive me if this is a silly question. Our new installation of GBrowse is not working and it looks like it will take me a while to figure out exactly what is going on. We have a conference coming up in 9 days at which we need to display some BAM files on our GBrowse. Our old GBrowse is on a very old machine that is desperately in need of patching and is getting errors when I attempt to build Bio::DB::Sam on it.  I very much doubt I will be able to display the BAM files on either machine by the time the conference happens. I will keep trying and I'll e-mail the gbrowse mailing list just in case someone can help with the errors installing Bio::DB::Sam.

We are running VMWare on our new servers and I noticed you provide .ova VMs that have a working GBrowse. I'm not sure what security risks or other issues might be involved in using one of these machines (even temporarily) in place of our current GBrowse VM, but I thought I would ask, just in case it can be done.

Thanks,

Jacqueline Lee
Xenbase Bioinformatician/ Software Developer
e-mail: [hidden email]<mailto:[hidden email]>
www.xenbase.org

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Message: 2
Date: Wed, 14 Aug 2013 10:10:36 -0600
From: Jacqueline Lee <[hidden email]>
Subject: [Gmod-gbrowse] Bio::DB::Sam issues
To: "'[hidden email]'"
        <[hidden email]>
Message-ID:
        <[hidden email]>

Content-Type: text/plain; charset="iso-8859-1"

Hello,

I've tried to build and install Bio::DB::Sam on two different GBrowse servers. I can run Build.PL, but when I actually try to run ./Build I get the following error:

/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

I'm not sure at all what could be causing this. I am using samtools 0.1.18 and it installed correctly.

The entire output is below:

Building Bio-SamTools
gcc -I/usr/local/src/samtools-0.1.18 -Ic_bin -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.38" -DVERSION="1.38" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_open?:
lib/Bio/DB/Sam.c:547: warning: unused variable ?packname?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_index_build?:
lib/Bio/DB/Sam.c:605: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_sort_core?:
lib/Bio/DB/Sam.xs:322: warning: implicit declaration of function ?bam_sort_core?
lib/Bio/DB/Sam.c:629: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_tell?:
lib/Bio/DB/Sam.xs:364: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:366: warning: format ?%llu? expects type ?long long unsigned int?, but argument 5 has type ?int64_t?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_qseq?:
lib/Bio/DB/Sam.xs:516: warning: operation on ?seq? may be undefined
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment__qscore?:
lib/Bio/DB/Sam.xs:530: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux?:
lib/Bio/DB/Sam.xs:589: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__builtin___strncat_chk? differ in signedness
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__strncat_ichk? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux_keys?:
lib/Bio/DB/Sam.xs:685: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_data?:
lib/Bio/DB/Sam.xs:708: warning: pointer targets in assignment differ in signedness
lib/Bio/DB/Sam.xs:711: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Header_view1?:
lib/Bio/DB/Sam.xs:914: warning: implicit declaration of function ?bam_view1?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam__Index_coverage?:
lib/Bio/DB/Sam.xs:999: warning: unused variable ?cov?
lib/Bio/DB/Sam.c: In function ?invoke_pileup_callback_fun?:
lib/Bio/DB/Sam.xs:149: warning: control reaches end of non-void function
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/local/src/samtools-0.1.18 -lbam -lpthread -lz
/usr/bin/ld: /usr/local/src/samtools-0.1.18/libbam.a(bgzf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

If anyone has an idea of how to fix this, it would be appreciated.

Thank you,
Jacqueline Lee
Xenbase Bioinformatician/ Software Developer
e-mail: [hidden email]<mailto:[hidden email]>
www.xenbase.org

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Message: 3
Date: Wed, 14 Aug 2013 10:21:20 -0600
From: Jacqueline Lee <[hidden email]>
Subject: Re: [Gmod-gbrowse] Bio::DB::Sam issues
To: "'[hidden email]'"
        <[hidden email]>
Message-ID:
        <[hidden email]>

Content-Type: text/plain; charset="iso-8859-1"

Hello,

Almost immediately after I sent this, I found the solution at http://www.linuxquestions.org/questions/linux-software-2/failed-to-install-sam-pm-884016/.

I hadn't compiled my libbam.a with -fPIC, so I needed to add the flag to my Makefile in my $SAMTOOLS directory.

Jacqueline

From: Jacqueline Lee
Sent: Wednesday, August 14, 2013 10:11 AM
To: '[hidden email]'
Subject: Bio::DB::Sam issues

Hello,

I've tried to build and install Bio::DB::Sam on two different GBrowse servers. I can run Build.PL, but when I actually try to run ./Build I get the following error:

/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

I'm not sure at all what could be causing this. I am using samtools 0.1.18 and it installed correctly.

The entire output is below:

Building Bio-SamTools
gcc -I/usr/local/src/samtools-0.1.18 -Ic_bin -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.38" -DVERSION="1.38" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_open?:
lib/Bio/DB/Sam.c:547: warning: unused variable ?packname?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam_index_build?:
lib/Bio/DB/Sam.c:605: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_sort_core?:
lib/Bio/DB/Sam.xs:322: warning: implicit declaration of function ?bam_sort_core?
lib/Bio/DB/Sam.c:629: warning: unused variable ?packname?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam_tell?:
lib/Bio/DB/Sam.xs:364: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:366: warning: format ?%llu? expects type ?long long unsigned int?, but argument 5 has type ?int64_t?
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_qseq?:
lib/Bio/DB/Sam.xs:516: warning: operation on ?seq? may be undefined
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment__qscore?:
lib/Bio/DB/Sam.xs:530: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux?:
lib/Bio/DB/Sam.xs:589: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__builtin___strncat_chk? differ in signedness
lib/Bio/DB/Sam.xs:613: warning: pointer targets in passing argument 2 of ?__strncat_ichk? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_aux_keys?:
lib/Bio/DB/Sam.xs:685: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Alignment_data?:
lib/Bio/DB/Sam.xs:708: warning: pointer targets in assignment differ in signedness
lib/Bio/DB/Sam.xs:711: warning: pointer targets in passing argument 2 of ?Perl_newSVpv? differ in signedness
lib/Bio/DB/Sam.xs: In function ?XS_Bio__DB__Bam__Header_view1?:
lib/Bio/DB/Sam.xs:914: warning: implicit declaration of function ?bam_view1?
lib/Bio/DB/Sam.c: In function ?XS_Bio__DB__Bam__Index_coverage?:
lib/Bio/DB/Sam.xs:999: warning: unused variable ?cov?
lib/Bio/DB/Sam.c: In function ?invoke_pileup_callback_fun?:
lib/Bio/DB/Sam.xs:149: warning: control reaches end of non-void function
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/local/src/samtools-0.1.18 -lbam -lpthread -lz
/usr/bin/ld: /usr/local/src/samtools-0.1.18/libbam.a(bgzf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/src/samtools-0.1.18/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 241.

If anyone has an idea of how to fix this, it would be appreciated.

Thank you,
Jacqueline Lee
Xenbase Bioinformatician/ Software Developer
e-mail: [hidden email]<mailto:[hidden email]>
www.xenbase.org<http://www.xenbase.org>

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Message: 4
Date: Thu, 15 Aug 2013 10:20:22 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] Bug? Balloon hover callback being called with
        2       different objects
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I'm currently building a new GBrowse instance with v2.55 and after copying across our old callback module I've found that I'm getting odd errors when call-backs are run on BAM track elements like:

An error occurred while evaluating the callback at section='812_PD4107a_bwa', option='balloon hover':
   => Can't locate object method "flag" via package "Bio::SeqFeature::Lite"

I did some digging and the problem that appears to be occurring is that the call back is being called twice once with the expected BAM object:

        Bio::DB::Bam::AlignWrapper

and then again with the unexpected:

        Bio::SeqFeature::Lite

I've prevented the spamming of my error logs by adding the following to the beginning of my call back:

        return unless($f->can('flag'));

I'm guessing that this is creating additional unnecessary load on the server so probably worth investigating.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

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




--
 The Wellcome Trust Sanger Institute is operated by Genome Rese arch  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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Message: 5
Date: Thu, 15 Aug 2013 10:34:34 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] balloon hover, can I turn it off in a semantic
        zoom?
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I have a BAM track configured with semantic zoom.

>From 1-150 bp I have a detailed popup of the read details and above that I want the balloons to not be rendered, e.g.:

[562_TR-1_RNA_ribozero_bwa]
...
balloon hover   = sub {&Sanger::CGP::GBrowse::GB_Init_Code::bam_tooltip(shift)}

[562_TR-1_RNA_ribozero_bwa:150]
balloon hover = 0

The problem I have is that even when 'ballon hover' is set to false a default ballonis generated (see attached).  Ideally I want to reduce the data being served and completely disable this behaviour at this zoom level.  I'm aware that this can be switched to a standard 'title' mouse over by changing 'titles are balloons', but I actually want the image map to be as minimal as possible.

Is it possible to completely turn off this feature?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

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




--
 The Wellcome Trust Sanger Institute is operated by Genome Rese arch  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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Message: 6
Date: Wed, 14 Aug 2013 16:45:56 -0400 (EDT)
From: Nic Herndon <[hidden email]>
Subject: [Gmod-gbrowse] Broken links on
        http://gmod.org/gbrowse2/tutorial/tutorial.html
To: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

The Generic Genome Browser Version 2: A Tutorial for Administrators at http://gmod.org/gbrowse2/tutorial/tutorial.html mentions a couple of directories that cannot be accessed: data_files (http://gmod.org/gbrowse2/tutorial/data_files/) and conf_files (http://gmod.org/gbrowse2/tutorial/conf_files/). When trying to access them the server returns the following error message.



Forbidden


You don't have permission to access /gbrowse2/tutorial/data_files/ on this server.


Apache/2.2.9 (Debian) PHP/5.2.6-1+lenny16 with Suhosin-Patch mod_ssl/2.2.9 OpenSSL/0.9.8g Server at gmod.org Port 80
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Message: 7
Date: Mon, 19 Aug 2013 15:01:00 -0400
From: Scott Cain <[hidden email]>
Subject: [Gmod-gbrowse] GMOD grant application letter of support
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="windows-1252"

 Hi all,

First, if you've already received this request, please accept my apologies; as you might imagine, I'm trying to blanket the world a few times over :-) I'm also working through the list of ?known? users of GMOD software, so you may get it again in the near future.

As you may have heard, we (Lincoln Stein, Ian Holmes and I) are applying for a grant to continue work on aspects of the GMOD project, particularly JBrowse and Chado development and GMOD coordination (standards, meetings and courses). We are applying for a community resources for genomics grant from the NIH:

http://grants.nih.gov/grants/guide/pa-files/PAR-11-095.html

for which we think GMOD is an excellent fit. One of the things we need to demonstrate for this grant is that we in fact support the community and have the support of the community, and one way we'd like to show that is with many letters of support. Would you be willing to write such a letter?
It could include information about how you've used or are planning to use GMOD software. To help you get started, I wrote some template paragraphs:

http://gmod.org/wiki/User:Scott#Support_letter_templates

The letters should be on institutional letterhead, signed and then scanned to a PDF or you could mail the original to me and I'll scan them.

The deadline for getting the letters of support back to me is September 3.
Please let me know if you're willing to write one and if there is anything I can do to help you.

Thanks so much,
Scott

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
Ontario Institute for Cancer Research
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Message: 8
Date: Wed, 21 Aug 2013 12:49:51 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] getting balloon click to use the URL generated
        by      'link = AUTO'
To: "Gbrowse (E-mail)" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I'm trying to get balloon click to use the URL generated by the AUTO option that can be applied to the link option.

I could construct the URL but I can't figure out where I would get the datasource component of the URL:

e.g. 'link = AUTO' generates this:

http://.../gbrowse_details/PD10021_37_58?ref=12;start=25358182;end=25403854;name=KRAS;class=Sequence;feature_id=242107;db_id=REFSEQ%3Adatabase

And I can construct the following which gives the same page, but how can I determine the source (in red)?

balloon click = http://.../gbrowse_details/PD10021_37_58?name=$name;feature_id=$id;db_id=REFSEQ%3Adatabase

or

balloon click = url:../../gbrowse_details/PD10021_37_58?name=$name;feature_id=$id;db_id=REFSEQ%3Adatabase

Am I going about this the wrong way?

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

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




--
 The Wellcome Trust Sanger Institute is operated by Genome Rese arch  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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End of Gmod-gbrowse Digest, Vol 87, Issue 6
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Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central is your source for news, insights,
analysis and resources for efficient Application Performance Management.
Visit us today!
http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
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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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