gbrowse installation problem

[Kie Kyon Huang]

hi all,

I am trying to install gbrowse on a cygwin environment running on windows.
i run the gbrowse_netinstall.pl from
http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/bin/gbrowse_netinstall.pl.

for some reason, it always end up like this

Installing Win32 perl module

Installing make utility...
Couldn't install nmake.exe: No such file or directory at gbrowse_netinstall.pl l
ine 150.
BEGIN failed--compilation aborted at gbrowse_netinstall.pl line 158.

how do I solve this?

Thanks a lot

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[Matthew Hobbs-2]

Sounds as if you're not using cygwin's perl. Did you run 'perl
gbrowse_netinstall.pl' from within a cygwin shell?

> -----Original Message-----
> From: Kie Kyon Huang [mailto:kiekyon.huang@...]
> Sent: Friday, 30 October 2009 12:00 PM
> To: gmod-gbrowse@...
> Subject: [Gmod-gbrowse] gbrowse installation problem
>
> hi all,
>
> I am trying to install gbrowse on a cygwin environment running on
> windows.
> i run the gbrowse_netinstall.pl from
> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-
> Browser/trunk/bin/gbrowse_netinstall.pl.
>
> for some reason, it always end up like this
>
> Installing Win32 perl module
>
> Installing make utility...
> Couldn't install nmake.exe: No such file or directory at
> gbrowse_netinstall.pl l
> ine 150.
> BEGIN failed--compilation aborted at gbrowse_netinstall.pl line 158.

___________________________________________
Matthew Hobbs Ph.D.
Faculty of Veterinary Science
C01 - J.L. Shute
University of Sydney, NSW 2570, Australia
Phone: [phone] Fax: [phone]


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[Scott Cain-4]

Hello,

The netinstall script was not written to use cygwin.  The last time I
tried cygwin (which was several years ago), it was impossible to get
GBrowse running.  I don't remember what the problem was, and it may
not be a problem any more.

The problem with the netinstall script is that it checks for the
operating system, and detecting that it is Windows, checks for nmake.
It doesn't find it and tries to install it, but since you aren't
running from cmd, it fails.  The best thing to do is to get the
GBrowse tarball from sourceforge

  http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-1.70/Generic-Genome-Browser-1.70.tar.gz/download

and do a manual install.  That is, unpack the tarball, and run perl
Makefile.PL, make and make install.  Running perl Makefile.PL will
almost certainly guess the wrong installation directories, so be sure
to enter the right places for your htdocs, cgi-bin, and apache conf
directories.

Good luck!
Scott



On Thu, Oct 29, 2009 at 8:59 PM, Kie Kyon Huang <kiekyon.huang@...> wrote:

> hi all,
>
> I am trying to install gbrowse on a cygwin environment running on windows.
> i run the gbrowse_netinstall.pl from
> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/bin/gbrowse_netinstall.pl.
>
> for some reason, it always end up like this
>
> Installing Win32 perl module
>
> Installing make utility...
> Couldn't install nmake.exe: No such file or directory at gbrowse_netinstall.pl l
> ine 150.
> BEGIN failed--compilation aborted at gbrowse_netinstall.pl line 158.
>
> how do I solve this?
>
> Thanks a lot
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> 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

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[Matthew Hobbs-2]

For the record, it is now possible to run gbrowse under cygwin. I am
happily running gbrowse 1.71b under cygwin and find it preferable (e.g.
no more problems with horrible Windows \-separated pathnames in config
files) to the usual Windows installation done with ActiveState perl etc.
However I haven't used the net installer.

> -----Original Message-----
> The netinstall script was not written to use cygwin.  The last time I
> tried cygwin (which was several years ago), it was impossible to get
> GBrowse running.  I don't remember what the problem was, and it may
> not be a problem any more.


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[Scott Cain-4]

Oh, I had no idea.  That's interesting and I'm glad it's working for
you.  I can definitely see how it would be preferable to use something
unix-like over Windows.  Maybe sometime in the next few weeks I'll get
a chance to install cygwin and try modifying the net installer.  Do
you know what the default locations for the Apache directories are in
cygwin?

Thanks,
Scott


On Thu, Oct 29, 2009 at 10:03 PM, Matthew Hobbs
<Matthew.Hobbs@...> wrote:

> For the record, it is now possible to run gbrowse under cygwin. I am
> happily running gbrowse 1.71b under cygwin and find it preferable (e.g.
> no more problems with horrible Windows \-separated pathnames in config
> files) to the usual Windows installation done with ActiveState perl etc.
> However I haven't used the net installer.
>
>> -----Original Message-----
>> The netinstall script was not written to use cygwin.  The last time I
>> tried cygwin (which was several years ago), it was impossible to get
>> GBrowse running.  I don't remember what the problem was, and it may
>> not be a problem any more.
>
>

--
------------------------------------------------------------------------
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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[Kie Kyon Huang]

ok, now i had this

 http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-1.70/Generic-Genome-Browser-1.70.tar.gz/download

and try to install manually on cygwin.  i am still facing problem when
i run 'make' and get the following error

Makefile:1184: *** multiple target patterns.  Stop.

the line 1184 on my Makefile.PL is

$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)

and also, i've tried installing on windows using the netinstall, but i
get the same error with the previous attempt on cygwin, that is

Installing Win32 perl module

Installing make utility...
Couldn't install nmake.exe: No such file or directory at gbrowse_netinstall.pl l
ine 150.
BEGIN failed--compilation aborted at gbrowse_netinstall.pl line 158.

thanks

On Fri, Oct 30, 2009 at 10:57 AM, Scott Cain <scott@...> wrote:

> Oh, I had no idea.  That's interesting and I'm glad it's working for
> you.  I can definitely see how it would be preferable to use something
> unix-like over Windows.  Maybe sometime in the next few weeks I'll get
> a chance to install cygwin and try modifying the net installer.  Do
> you know what the default locations for the Apache directories are in
> cygwin?
>
> Thanks,
> Scott
>
>
> On Thu, Oct 29, 2009 at 10:03 PM, Matthew Hobbs
> <Matthew.Hobbs@...> wrote:
>> For the record, it is now possible to run gbrowse under cygwin. I am
>> happily running gbrowse 1.71b under cygwin and find it preferable (e.g.
>> no more problems with horrible Windows \-separated pathnames in config
>> files) to the usual Windows installation done with ActiveState perl etc.
>> However I haven't used the net installer.
>>
>>> -----Original Message-----
>>> The netinstall script was not written to use cygwin.  The last time I
>>> tried cygwin (which was several years ago), it was impossible to get
>>> GBrowse running.  I don't remember what the problem was, and it may
>>> not be a problem any more.
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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[Matthew Hobbs-2]

Hi again,

I'm sure installation with gbrowse_netinstall.pl would be the easier of
the two Windows installation routes once you overcome the nmake problem,
but I can't help with this I'm afraid (over to you Scott...).

However if you're sure you want to try installing under cygwin (it can
be done!) this is the only help I can offer:

You must have the cygwin perl package installed, you must use cygwin's
perl to create the Makefile, and you must use cygwin's make to build and
install. Is it possible you have a Makefile that was created by your
non-cygwin perl during an earlier installation attempt? If there are
Windows-style pathnames in there that might cause the 'multiple target
patterns' error. e.g. my Makefile has lines like this:

PERL_ARCHLIB = /usr/lib/perl5/5.8/cygwin

Any paths in there like e.g.:

C:\Perl\Lib\ etc

are no good!

Of course make sure cygwin's perl has all the required modules (see
http://gmod.org/wiki/GBrowse_Install_HOWTO).

So my suggestions - make sure you have the cygwin perl, use CPAN to
install required modules, remove the old Makefile, and rerun 'perl
Makefile.PL'. In fact why not do '/usr/bin/perl Makefile.PL' (to make
sure you're using cygwin's perl).

There are other cygwin packages necessary but I'm afraid I haven't got a
list of them. They should become obvious as errors arise! I'm sure
you'll need perl and make, and think you'll need these too (the versions
are what I happen to have, there may be more recent ones available):


gcc4                    4.3.2-2            
libgd2                  2.0.36RC1-1        
gzip                    1.3.12-2          
tar                     1.21-1            

You will probably want these too for a cygwin apache server :

apache2                 2.2.6-1            OK
apache2-devel           2.2.6-1            OK

Good luck,

Matthew

> -----Original Message-----
> From: Kie Kyon Huang [mailto:kiekyon.huang@...]
> Sent: Sunday, 1 November 2009 2:52 PM
> To: Scott Cain
> Cc: Matthew Hobbs; gmod-gbrowse@...
> Subject: Re: [Gmod-gbrowse] gbrowse installation problem
>
> ok, now i had this
>
>
>

http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/G

> Browse-1.70/Generic-Genome-Browser-1.70.tar.gz/download
>
> and try to install manually on cygwin.  i am still facing problem when
> i run 'make' and get the following error
>
> Makefile:1184: *** multiple target patterns.  Stop.
>
> the line 1184 on my Makefile.PL is
>
> $(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
>
> and also, i've tried installing on windows using the netinstall, but i
> get the same error with the previous attempt on cygwin, that is
>
> Installing Win32 perl module
>
> Installing make utility...
> Couldn't install nmake.exe: No such file or directory at
> gbrowse_netinstall.pl l
> ine 150.
> BEGIN failed--compilation aborted at gbrowse_netinstall.pl line 158.
>
> thanks
>

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