[Bioperl-l] New Fink Bioperl dependency installer, etc., Bio::Graphics on Mac OS X
Gudmundur Arni Thorisson
mummi@cshl.org
Wed, 4 Sep 2002 13:36:38 -0400
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I have something to add to this Fink/Mac OS X discussion, even though=20=
the Bio::Graphics package from the GMOD project (http://www.gmod.org/) =
isn=B4
t strictly part of Bioperl itself. I have recently installed =
Bio::Graphics=20
on Mac OS X 10.1.5. I had had some problems with the GD.pm/gd library=20
installation, as the Fink-managed gd libs wouldn=B4t install properly a =
few=20
months ago. But after reading Steven=B4s E-mail about Fink and OS X, I=20=
tried again, did =B4fink update gd=B4 and then tried to run =
Bio::Graphics=20
tests =3D> VOILA. So, at least in my case, it seems to work fine now. I =
have=20
however not yet completely installed the GMOD GBrowse interface on OS X,=20=
but that will be the next step.
PS this message is cross-posted to the GMOD developers list.
PSS I have had the same problem with updating Perl itself and CPAN =
Bundle.
Never seems to work properly, so I've just given up on trying to =
manually=20
install Perl this way. I just use whatever Apple feeds me!
Mummi, CSHL
--
------------------------------------------------
Gudmundur Arni Thorisson, bioinformatics researcher
Steinlab, Cold Spring Harbor Laboratory
w-phone#: 516-367-6904
w-fax#: 516-367-8389
1 Bungtown Road
Cold Spring Harbor
11724 New York
USA
On Wednesday, September 4, 2002, at 11:29 AM, Steven Cannon wrote:
> I've been maintaining a site describing my Bioperl install experiences =
on=20
> Mac OS X ( http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html ),=20=
> and would like to keep it up to date by getting feedback from other OS =
X=20
> users. In particular, there are two install options that I would like =
to=20
> hear more about: the CPAN.pm BioPerl::Bundle, and a new Fink Bioperl=20=
> dependency installer by Christopher Dithi (Thanks! - this should be an=20=
> ideal solution for OS X).
>
> There is an OS X - specific problem with CPAN (see below). The Fink=20
> "bioperl-pm" is currently in the "unstable" branch, meaning that it =
needs=20
> more testing. I would also like to know whether the new version of the =
OS=20
> (10.2) causes any problems, either in existing or new installations. =
Here'
> s what I say on my page -- and I'll update this as I hear other =
peoples'=20
> experiences with CPAN or Fink.
> =3D=3D=3D
> There are at least three quite distinct options for installing the=20
> BioPerl dependencies on OS X. You can 1) do it "from scratch," =
following=20
> the instructions on this page, or 2) you can use the CPAN.pm module =
and=20
> BioPerl::Bundle, which should install almost all of the dependencies=20=
> nearly automatically, or 3) you can try the new Fink bioperl-pm =
package,=20
> which also should install almost all of the dependencies nearly=20
> automatically. Unfortunately, none of these options is entirely =
without a=20
> certain amount of hassle and risk. In order, here are the options in =
more=20
> detail:
>
> 1) Doing the installations manually gives you the most control, but =
there=20
> are a few pitfalls here and there (particularly, see the note about =
"HEAD"
> below, under "LWP.")
>
> 2) CPAN.pm is a wonderful creation, but I have been frustrated by it =
on=20
> OS X. In particular, the last time I tried to install CPAN.pm itself =
(in=20
> July, 2002), it tried to update my version of Perl to 5.80 -- which =
would=20
> seem like a virtuous thing, but the Perl reinstallation process itself=20=
> was long and arduous, and didn't work for me (it caused me no problems=20=
> with the default installation, but 5.80 didn't "take.") And then when =
I=20
> tried to use it to install BioPerl::Bundle, it tried AGAIN (and =
without=20
> asking or giving me the option to refuse) to install 5.80. That said, =
the=20
> dependencies did install correctly. However, unless someone knows how =
to=20
> circumvent this problem, I can't recommend BioPerl::Bundle on OS X. =
(And=20
> if someone knows a way around this problem, please let me know! =
Actually,
> to investigate, try =
http://www.scriptdigital.com/divers/frontiermonitor.
> html -- which looks like a solution).
>
> 3) The Fink option should be the best solution, because the Fink =
package=20
> manager is explicitly designed for OS X. It also installs everything =
in=20
> its own private directory (/sw), so there is essentially no danger of=20=
> overwriting important Unix utilities and libraries. The bioperl-pm=20
> package is new, and I haven't tested it, so I (and the package =
maintainer,
> Christopher Dithi) would be interested to hear how it goes. As of =
August,
> 2002, the Fink bioperl-pm is in the "unstable" branch, meaning that =
it=20
> has not been well tested. You can help!
> =3D=3D=3D
> - Steven Cannon
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
>
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I have something to add to this Fink/Mac OS X discussion, even
though the Bio::Graphics package from the GMOD project
(http://www.gmod.org/) isn=B4t strictly part of Bioperl itself. I have
recently installed Bio::Graphics on Mac OS X 10.1.5. I had had some
problems with the GD.pm/gd library installation, as the Fink-managed
gd libs wouldn=B4t install properly a few months ago. But after reading
Steven=B4s E-mail about Fink and OS X, I tried again, did =B4fink =
update
gd=B4 and then tried to run Bio::Graphics tests =3D> VOILA. So, at least
in my case, it seems to work fine now. I have however not yet
completely installed the GMOD GBrowse interface on OS X, but that will
be the next step.
PS this message is cross-posted to the GMOD developers list.
PSS I have had the same problem with updating Perl itself and CPAN
Bundle. Never seems to work properly, so I've just given up on trying
to manually install Perl this way. I just use whatever Apple feeds me!
Mummi, CSHL
<fontfamily><param>Courier</param>--
------------------------------------------------
Gudmundur Arni Thorisson, bioinformatics researcher
Steinlab, Cold Spring Harbor Laboratory
w-phone#: 516-367-6904
w-fax#: 516-367-8389
1 Bungtown Road
Cold Spring Harbor
11724 New York
USA
</fontfamily>
On Wednesday, September 4, 2002, at 11:29 AM, Steven Cannon wrote:
<excerpt>I've been maintaining a site describing my Bioperl install
experiences on Mac OS X (
http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html ), and would
like to keep it up to date by getting feedback from other OS X users.
In particular, there are two install options that I would like to hear
more about: the CPAN.pm BioPerl::Bundle, and a new Fink Bioperl
dependency installer by Christopher Dithi (Thanks! - this should be an
ideal solution for OS X).
There is an OS X - specific problem with CPAN (see below). The Fink
"bioperl-pm" is currently in the "unstable" branch, meaning that it
needs more testing. I would also like to know whether the new version
of the OS (10.2) causes any problems, either in existing or new
installations. Here's what I say on my page -- and I'll update this as
I hear other peoples' experiences with CPAN or Fink.
=3D=3D=3D
There are at least three quite distinct options for installing the
BioPerl dependencies on OS X. You can 1) do it "from scratch,"
following the instructions on this page, or 2) you can use the CPAN.pm
module and BioPerl::Bundle, which should install almost all of the
dependencies nearly automatically, or 3) you can try the new Fink
bioperl-pm package, which also should install almost all of the
dependencies nearly automatically. Unfortunately, none of these
options is entirely without a certain amount of hassle and risk. In
order, here are the options in more detail:
1) Doing the installations manually gives you the most control, but
there are a few pitfalls here and there (particularly, see the note
about "HEAD" below, under "LWP.")
2) CPAN.pm is a wonderful creation, but I have been frustrated by it
on OS X. In particular, the last time I tried to install CPAN.pm
itself (in July, 2002), it tried to update my version of Perl to 5.80
-- which would seem like a virtuous thing, but the Perl reinstallation
process itself was long and arduous, and didn't work for me (it caused
me no problems with the default installation, but 5.80 didn't "take.")
And then when I tried to use it to install BioPerl::Bundle, it tried
AGAIN (and without asking or giving me the option to refuse) to
install 5.80. That said, the dependencies did install correctly.
However, unless someone knows how to circumvent this problem, I can't
recommend BioPerl::Bundle on OS X. (And if someone knows a way around
this problem, please let me know! Actually, to investigate, try
http://www.scriptdigital.com/divers/frontiermonitor.html -- which
looks like a solution).
3) The Fink option should be the best solution, because the Fink
package manager is explicitly designed for OS X. It also installs
everything in its own private directory (/sw), so there is essentially
no danger of overwriting important Unix utilities and libraries. The
bioperl-pm package is new, and I haven't tested it, so I (and the
package maintainer, Christopher Dithi) would be interested to hear how
it goes. As of August, 2002, the Fink bioperl-pm is in the "unstable"
branch, meaning that it has not been well tested. You can help!
=3D=3D=3D
- Steven Cannon
_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l
</excerpt>=
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