Bio::DB::BigFile

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Bio::DB::BigFile

Nathaniel Street
Hi

I'm having problems installing Bio::DB::BigFile. I have downloaded and compiled the kent source as in the instructions. I can see bigWig.h in the src/inc directory and I have jkweb.a in src/lib/i686. When prompted for the kent src location for the BigFile install I enter the path (/home/nat/work/software/kent/src) but get the error

Can't find the bigWig.h and jkweb.a files at this location.

I've tried other paths e.g. src/lib src/lib/i686 etc but nothing works.

I'm obviously doing somthing stupid but I can't see what it is. Can anyone help?

Thanks

Nathaniel
--
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
SE901-87 Umeå
SWEDEN

email: [hidden email]
skype: nathaniel_street
tel: 0046907865473
fax:  0046907866676

www.popgenie.org


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Re: Bio::DB::BigFile

Fields, Christopher J
Make sure to export MACHTYPE to match whatever you compiled the kent source tree into (generally, something like 'x86', 'x86_64', etc).  See here (under TROUBLESHOOTING).  

http://cpansearch.perl.org/src/LDS/Bio-BigFile-1.03/README

In the kent source tree, the instructions for building are in src/product/README.building.source.

chris

On Sep 29, 2010, at 2:32 AM, Nathaniel Street wrote:

> Hi
>
> I'm having problems installing Bio::DB::BigFile. I have downloaded and compiled the kent source as in the instructions. I can see bigWig.h in the src/inc directory and I have jkweb.a in src/lib/i686. When prompted for the kent src location for the BigFile install I enter the path (/home/nat/work/software/kent/src) but get the error
>
> Can't find the bigWig.h and jkweb.a files at this location.
>
> I've tried other paths e.g. src/lib src/lib/i686 etc but nothing works.
>
> I'm obviously doing somthing stupid but I can't see what it is. Can anyone help?
>
> Thanks
>
> Nathaniel
> --
> Nathaniel Street
> Umeå Plant Science Centre
> Department of Plant Physiology
> Umeå University
> SE901-87 Umeå
> SWEDEN
>
> email: [hidden email]
> skype: nathaniel_street
> tel: 0046907865473
> fax:  0046907866676
>
> www.popgenie.org
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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Re: Bio::DB::BigFile

Nathaniel Street
Thanks for the reply. I discovered my problem and, of course, I was being stupid - so here's where I went wrong in case anyone else makes the same mistake.

I compiled the kent source as 'me' i.e. not sudo so MACHTYPE was set only for me. I then ran sudo ./build and of course MACHTYPE was no longer set.

I also found that I had to compile the kent source using 'make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC' because otherwise I got an error about shared libraries.

This was all on Ubuntu (10.1)

Nat

On Sep 29, 2010, at 5:59 PM, Chris Fields wrote:

> Make sure to export MACHTYPE to match whatever you compiled the kent source tree into (generally, something like 'x86', 'x86_64', etc).  See here (under TROUBLESHOOTING).  
>
> http://cpansearch.perl.org/src/LDS/Bio-BigFile-1.03/README
>
> In the kent source tree, the instructions for building are in src/product/README.building.source.
>
> chris
>
> On Sep 29, 2010, at 2:32 AM, Nathaniel Street wrote:
>
>> Hi
>>
>> I'm having problems installing Bio::DB::BigFile. I have downloaded and compiled the kent source as in the instructions. I can see bigWig.h in the src/inc directory and I have jkweb.a in src/lib/i686. When prompted for the kent src location for the BigFile install I enter the path (/home/nat/work/software/kent/src) but get the error
>>
>> Can't find the bigWig.h and jkweb.a files at this location.
>>
>> I've tried other paths e.g. src/lib src/lib/i686 etc but nothing works.
>>
>> I'm obviously doing somthing stupid but I can't see what it is. Can anyone help?
>>
>> Thanks
>>
>> Nathaniel
>> --
>> Nathaniel Street
>> Umeå Plant Science Centre
>> Department of Plant Physiology
>> Umeå University
>> SE901-87 Umeå
>> SWEDEN
>>
>> email: [hidden email]
>> skype: nathaniel_street
>> tel: 0046907865473
>> fax:  0046907866676
>>
>> www.popgenie.org
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
SE901-87 Umeå
SWEDEN

email: [hidden email]
skype: nathaniel_street
tel: 0046907865473
fax:  0046907866676

www.popgenie.org


------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
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Re: Bio::DB::BigFile

Fields, Christopher J
On Sep 29, 2010, at 11:34 AM, Nathaniel Street wrote:

> Thanks for the reply. I discovered my problem and, of course, I was being stupid - so here's where I went wrong in case anyone else makes the same mistake.

np

> I compiled the kent source as 'me' i.e. not sudo so MACHTYPE was set only for me. I then ran sudo ./build and of course MACHTYPE was no longer set.
>
> I also found that I had to compile the kent source using 'make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC' because otherwise I got an error about shared libraries.
>
> This was all on Ubuntu (10.1)
>
> Nat

I recall something along these lines, but my solution was a bit difference (I think it involved removing -Werror in the makefile, which I think is described in the UCSC docs somewhere).  The use of -fPIC makes more sense, though.

chris

> On Sep 29, 2010, at 5:59 PM, Chris Fields wrote:
>
>> Make sure to export MACHTYPE to match whatever you compiled the kent source tree into (generally, something like 'x86', 'x86_64', etc).  See here (under TROUBLESHOOTING).  
>>
>> http://cpansearch.perl.org/src/LDS/Bio-BigFile-1.03/README
>>
>> In the kent source tree, the instructions for building are in src/product/README.building.source.
>>
>> chris
>>
>> On Sep 29, 2010, at 2:32 AM, Nathaniel Street wrote:
>>
>>> Hi
>>>
>>> I'm having problems installing Bio::DB::BigFile. I have downloaded and compiled the kent source as in the instructions. I can see bigWig.h in the src/inc directory and I have jkweb.a in src/lib/i686. When prompted for the kent src location for the BigFile install I enter the path (/home/nat/work/software/kent/src) but get the error
>>>
>>> Can't find the bigWig.h and jkweb.a files at this location.
>>>
>>> I've tried other paths e.g. src/lib src/lib/i686 etc but nothing works.
>>>
>>> I'm obviously doing somthing stupid but I can't see what it is. Can anyone help?
>>>
>>> Thanks
>>>
>>> Nathaniel
>>> --
>>> Nathaniel Street
>>> Umeå Plant Science Centre
>>> Department of Plant Physiology
>>> Umeå University
>>> SE901-87 Umeå
>>> SWEDEN
>>>
>>> email: [hidden email]
>>> skype: nathaniel_street
>>> tel: 0046907865473
>>> fax:  0046907866676
>>>
>>> www.popgenie.org
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Start uncovering the many advantages of virtual appliances
>>> and start using them to simplify application deployment and
>>> accelerate your shift to cloud computing.
>>> http://p.sf.net/sfu/novell-sfdev2dev
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
> --
> Nathaniel Street
> Umeå Plant Science Centre
> Department of Plant Physiology
> Umeå University
> SE901-87 Umeå
> SWEDEN
>
> email: [hidden email]
> skype: nathaniel_street
> tel: 0046907865473
> fax:  0046907866676
>
> www.popgenie.org
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
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