From biopython at maubp.freeserve.co.uk  Mon Sep  7 07:56:17 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Sep 2009 12:56:17 +0100
Subject: [emboss-dev] Anonymous CVS working again :)
Message-ID: <320fb6e00909070456k28122011o59bfb3d640c4a0a8@mail.gmail.com>

Just an FYI,

While the developer server dev.open-bio.org has been fine, recently
our public read only mirror at cvs.open-bio.org (and cvs.biopython.org)
had not been updated. This affected Biopython and EMBOSS.

And for Biopython as a knock on effect, this had meant the latest
code at http://biopython.org/SRC/biopython/ was a little out of date.
[Biopython's github mirror was not affected]

These all seem to be working fine once again - thanks to someone
at the OBF - let me know who and I'll buy you a beer when we (next)
meet up :)

Peter

From jbdundas at gmail.com  Mon Sep  7 15:36:47 2009
From: jbdundas at gmail.com (jitesh dundas)
Date: Tue, 8 Sep 2009 01:06:47 +0530
Subject: [emboss-dev] emboss-dev Digest, Vol 13, Issue 1
In-Reply-To: <mailman.7.1252339203.7270.emboss-dev@lists.open-bio.org>
References: <mailman.7.1252339203.7270.emboss-dev@lists.open-bio.org>
Message-ID: <326ea8620909071236h4ce36fc7rce138806e65e6980@mail.gmail.com>

Dear Sir,/Madam,

I apologize for the inactivity on my part..
I am implementing the Parallel Java API for emboss.

The issue is that I don't know how to implement in Emboss...

Te implementation can be done at code level or thread level..

I need some help in doing so in Emboss.

Can anyone help me in this. I have limited know-how of emboss source-code...

Regards,
Jitesh Dundas

On 9/7/09, emboss-dev-request at lists.open-bio.org
<emboss-dev-request at lists.open-bio.org> wrote:
> Send emboss-dev mailing list submissions to
>  emboss-dev at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>  http://lists.open-bio.org/mailman/listinfo/emboss-dev
> or, via email, send a message with subject or body 'help' to
>  emboss-dev-request at lists.open-bio.org
>
> You can reach the person managing the list at
>  emboss-dev-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of emboss-dev digest..."
>
>
> Today's Topics:
>
>    1. Anonymous CVS working again :) (Peter)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 7 Sep 2009 12:56:17 +0100
> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: [emboss-dev] Anonymous CVS working again :)
> To: Biopython-Dev Mailing List <biopython-dev at lists.open-bio.org>,
>  emboss-dev at lists.open-bio.org
> Cc: root-l at lists.open-bio.org
> Message-ID:
>  <320fb6e00909070456k28122011o59bfb3d640c4a0a8 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Just an FYI,
>
> While the developer server dev.open-bio.org has been fine, recently
> our public read only mirror at cvs.open-bio.org (and cvs.biopython.org)
> had not been updated. This affected Biopython and EMBOSS.
>
> And for Biopython as a knock on effect, this had meant the latest
> code at http://biopython.org/SRC/biopython/ was a little out of date.
> [Biopython's github mirror was not affected]
>
> These all seem to be working fine once again - thanks to someone
> at the OBF - let me know who and I'll buy you a beer when we (next)
> meet up :)
>
> Peter
>
>
> ------------------------------
>
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>
>
> End of emboss-dev Digest, Vol 13, Issue 1
> *****************************************
>

From biopython at maubp.freeserve.co.uk  Mon Sep  7 16:00:46 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Sep 2009 21:00:46 +0100
Subject: [emboss-dev] [Root-l] Anonymous CVS working again :)
In-Reply-To: <B86883FE-D894-4933-81AE-7D5452075301@illinois.edu>
References: <320fb6e00909070456k28122011o59bfb3d640c4a0a8@mail.gmail.com>
	<B86883FE-D894-4933-81AE-7D5452075301@illinois.edu>
Message-ID: <320fb6e00909071300x6238e828l4440e71c562e792c@mail.gmail.com>

> Are these being kept in sync? ? bioperl's moved completely away from
> cvs to svn with very little pain. ?We found sync-ing the two more trouble
> than it was worth.

Perhaps we are talking at cross purposes here Chris.

Right now Biopython and EMBOSS are using CVS, with developers
committing to dev.open-bio.org, which then updates a read only CVS
mirror code.open-bio.org (aka cvs.open-bio.org aka cvs.biopython.org)
to provide anonymous assess.

Likewise, BioPerl etc are using SVN, with developers committing to
dev.open-bio.org, which then updates a read only SVN mirror at
code.open-bio.org (or its other aliases) to provide anonymous assess.

Peter


From biopython at maubp.freeserve.co.uk  Wed Sep  9 10:30:44 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Sep 2009 15:30:44 +0100
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
Message-ID: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>

Hi all,

I've read the instructions here and have been able to build
the core EMBOSS tools from CVS:
http://emboss.sourceforge.net/developers/cvs.html

However, I would also like to compile the EMBASSY tools,
in particular the PHYLIPNEW suite. Is this procedure
written down?

Thanks,

Peter

From uludag at ebi.ac.uk  Wed Sep  9 10:52:34 2009
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Wed, 09 Sep 2009 15:52:34 +0100
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
In-Reply-To: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
References: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
Message-ID: <1252507954.3070.83.camel@emboss2.ebi.ac.uk>


> I've read the instructions here and have been able to build
> the core EMBOSS tools from CVS:
> http://emboss.sourceforge.net/developers/cvs.html
> 
> However, I would also like to compile the EMBASSY tools,
> in particular the PHYLIPNEW suite. Is this procedure
> written down?

I found the following page by google search which looks relevant.

http://emboss.sourceforge.net/docs/adminguide/node28.html

New EMBOSS documentation have a slightly updated version with an
explanation for the case EMBOSS was not compiled beforehand but it has
not been published in EMBOSS official pages yet.

Regards,
Mahmut



From ajb at ebi.ac.uk  Wed Sep  9 11:18:26 2009
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 9 Sep 2009 16:18:26 +0100 (BST)
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
In-Reply-To: <1252507954.3070.83.camel@emboss2.ebi.ac.uk>
References: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
	<1252507954.3070.83.camel@emboss2.ebi.ac.uk>
Message-ID: <56792.86.26.12.63.1252509506.squirrel@webmail.ebi.ac.uk>

More up-to-date instructions are in the top level FAQ in the
CVS version.

I've just committed a slight fix to that file (it didn't
specify the flags for aclocal and automake - which are as you'd expect)
so it may take a couple of hours to be copied over to the public CVS.
Otherwise the file is pretty much the same as the FAQ from the
distribution.

ATB

Alan


>
>> I've read the instructions here and have been able to build
>> the core EMBOSS tools from CVS:
>> http://emboss.sourceforge.net/developers/cvs.html
>>
>> However, I would also like to compile the EMBASSY tools,
>> in particular the PHYLIPNEW suite. Is this procedure
>> written down?
>
> I found the following page by google search which looks relevant.
>
> http://emboss.sourceforge.net/docs/adminguide/node28.html
>
> New EMBOSS documentation have a slightly updated version with an
> explanation for the case EMBOSS was not compiled beforehand but it has
> not been published in EMBOSS official pages yet.
>
> Regards,
> Mahmut
>
>
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>



From biopython at maubp.freeserve.co.uk  Wed Sep  9 11:34:06 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Sep 2009 16:34:06 +0100
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
In-Reply-To: <4AA7C0CD.7020403@ebi.ac.uk>
References: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
	<4AA7C0CD.7020403@ebi.ac.uk>
Message-ID: <320fb6e00909090834w49dd3e53xee1a4d9f14770fdd@mail.gmail.com>

On Wed, Sep 9, 2009 at 3:50 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
>
> The installation is the same as for EMBOSS. You just need to cd to
> embassy/packagename
>
> cd embassy
> cd phylipnew
> aclocal -I m4
> autoconf
> automake -a
> ./configure (same options as you used for EMBOSS)
> make
> make install

Thanks.

I had tried that but there was a build problem, probably related to
my not yet having updated libtool on this machine.

So there is nothing like make-static-developers?

Peter C

From jbdundas at gmail.com  Sun Sep 13 07:13:22 2009
From: jbdundas at gmail.com (jitesh dundas)
Date: Sun, 13 Sep 2009 16:43:22 +0530
Subject: [emboss-dev] Can I help.
Message-ID: <326ea8620909130413x79c01f29g70280bc59dec7cda@mail.gmail.com>

Dear Sir/Madam,

I would like to contribute to this project. Is  there anything that I could
do to help..

Please let me know if you need anything else from my side..

Regards,
Jitesh Dundas

From biopython at maubp.freeserve.co.uk  Wed Sep 16 19:23:37 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Sep 2009 00:23:37 +0100
Subject: [emboss-dev] PHYLIP(NEW) and stdout
In-Reply-To: <320fb6e00909161614r288fb399o22328bbb4f4de230@mail.gmail.com>
References: <320fb6e00909161614r288fb399o22328bbb4f4de230@mail.gmail.com>
Message-ID: <320fb6e00909161623u4d4f2eb6s5dedb61b28308f74@mail.gmail.com>

Hi all,

Some years ago I filed bug 1587853 about fseqboot including "noisy"
output on stdout, which means it can't be used for bootstrapping where
the resampled alignments are sent to stdout (e.g. using the -filter or
-stdout arguments). e.g.

cat tiny.phy | fseqboot -reps 3 -filter

I've just found fdnadist has the same problem, in addition to the
distance matrices (the actual output) progress messages are also
printed to stdout (when using the -filter or -stdout arguments). e.g.

cat opuntia.fasta | fdnadist -method k -filter
fdnadist -sequence opuntia.fasta -method k -stdout -auto
fdnadist -sequence opuntia.fasta -method k -filter

I presume this is symptomatic of all the PHYLIPNEW tools, which is a
shame as it prevents piping their output together which to me is the
natural way to use these tools (rather than messing about with named
temporary files). It also spoils my plans for calling the PHYLIP tools
from Python and capturing their output via stdout (again, without
messing about with temp output files).

Would it be simple to make all these progress messages go to stderr
instead of stdout? Or just disable them if -stdout or -filter has been
used? I can appreciate that as you are wrapping a 3rd party tool here,
any EMBOSS specific changes should be kept to a minimum, so this
may not be that simple.

If no one other than me has asked about this, perhaps it isn't a big
issue for most EMBOSS+PHYLIP users?

Regards,

Peter C.

From pmr at ebi.ac.uk  Wed Sep 16 20:22:39 2009
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 17 Sep 2009 01:22:39 +0100
Subject: [emboss-dev] PHYLIP(NEW) and stdout
In-Reply-To: <320fb6e00909161623u4d4f2eb6s5dedb61b28308f74@mail.gmail.com>
References: <320fb6e00909161614r288fb399o22328bbb4f4de230@mail.gmail.com>
	<320fb6e00909161623u4d4f2eb6s5dedb61b28308f74@mail.gmail.com>
Message-ID: <4AB1814F.6060207@ebi.ac.uk>

Peter C. wrote:
> Hi all,
> 
> Some years ago I filed bug 1587853 about fseqboot including "noisy"
> output on stdout, which means it can't be used for bootstrapping where
> the resampled alignments are sent to stdout (e.g. using the -filter or
> -stdout arguments). e.g.
>
> Would it be simple to make all these progress messages go to stderr
> instead of stdout? Or just disable them if -stdout or -filter has been
> used? I can appreciate that as you are wrapping a 3rd party tool here,
> any EMBOSS specific changes should be kept to a minimum, so this
> may not be that simple.

Yes ... the phylip code is pretty clean and we could put something in to 
catch these messages with stdout as the default but some other output 
available as a command line option.

I just added the phylip 3.69 code changes in CVS. I will look into this 
when I am back next week.

regards,

Peter

From ajb at ebi.ac.uk  Wed Sep 23 07:17:06 2009
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 23 Sep 2009 12:17:06 +0100 (BST)
Subject: [emboss-dev] Major changes to AJAX structure in CVS
Message-ID: <43251.86.26.12.63.1253704626.squirrel@webmail.ebi.ac.uk>

Dear developers,

Major structural work has been done on the structure
of AJAX on the CVS server this morning. This is associated
with a future intention to move ACD functions into
a separate library. This will allow it to call sub-libraries
which will perform various new methods of data retrieval without
having to incorporate all those methods into one monolithic
libajax library.


As of today AJAX has the following subdirectories:

  pcre core graphics ensembl ajaxseq acd

pcre: file in here are the ones from the original ajax directory
      and compile to create a libepcre library.

core: currently contains all the aj*.c/h files from the original
      ajax directory with the exception of the graphics
      C files (some headers are left for the moment to
      avoid circular dependencies until ACD functions are moved).
      These files create a libajax library as before.

graphics: contains the ajgraph* and ajhist* files and, as before,
      create a libajaxg library

ensembl: New routines for accessing Ensembl. A work in progress.
      They create a libensembl library.

ajaxseq: A placeholder for ajax sequence handling source to be
     moved from core as part of the ACD changes. Currently
     this contains dummy source files and creates a
     libajaxseq library.

acd: A placeholder or the ACD functions to be moved. Currently this
     contains dummy source files and creates a libacd library.


These changes have, of course, required significant changes to
Makefile.am files thoughout EMBOSS and EMBASSY.


Given the major changes involved I'd recommend using a fresh
checkout of EMBOSS as you may have problems with
a "cvs update -dP" - old dependencies (etc) may still
exist in hidden directories (.libs/.deps/etc) which
could potentially mess things up. You should certainly
try a fresh checkout before emailing with related problems.


If you use the myemboss development area then the configuration for
that has been updated. If, however, you've made your own EMBASSY-style
packages then you'll need to modify your configuration using
one of the new Makefile.am files as a template.


A further change has been to add preliminary ajsql.c/h files
to AJAX. This has involved adding checks for MYSQL and POSTGRESQL
in the top level configuration (and two new m4 files in the m4
directory).

The configuration and compilation should be happy whether you have
both SQL development files installed, only one or none. However,
if you experience any problems in the compilation
in that area then please let me know.

The changes may take a couple of hours to propagate to the
anonymous CVS server.

Alan



From biopython at maubp.freeserve.co.uk  Mon Sep  7 11:56:17 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Sep 2009 12:56:17 +0100
Subject: [emboss-dev] Anonymous CVS working again :)
Message-ID: <320fb6e00909070456k28122011o59bfb3d640c4a0a8@mail.gmail.com>

Just an FYI,

While the developer server dev.open-bio.org has been fine, recently
our public read only mirror at cvs.open-bio.org (and cvs.biopython.org)
had not been updated. This affected Biopython and EMBOSS.

And for Biopython as a knock on effect, this had meant the latest
code at http://biopython.org/SRC/biopython/ was a little out of date.
[Biopython's github mirror was not affected]

These all seem to be working fine once again - thanks to someone
at the OBF - let me know who and I'll buy you a beer when we (next)
meet up :)

Peter


From jbdundas at gmail.com  Mon Sep  7 19:36:47 2009
From: jbdundas at gmail.com (jitesh dundas)
Date: Tue, 8 Sep 2009 01:06:47 +0530
Subject: [emboss-dev] emboss-dev Digest, Vol 13, Issue 1
In-Reply-To: <mailman.7.1252339203.7270.emboss-dev@lists.open-bio.org>
References: <mailman.7.1252339203.7270.emboss-dev@lists.open-bio.org>
Message-ID: <326ea8620909071236h4ce36fc7rce138806e65e6980@mail.gmail.com>

Dear Sir,/Madam,

I apologize for the inactivity on my part..
I am implementing the Parallel Java API for emboss.

The issue is that I don't know how to implement in Emboss...

Te implementation can be done at code level or thread level..

I need some help in doing so in Emboss.

Can anyone help me in this. I have limited know-how of emboss source-code...

Regards,
Jitesh Dundas

On 9/7/09, emboss-dev-request at lists.open-bio.org
<emboss-dev-request at lists.open-bio.org> wrote:
> Send emboss-dev mailing list submissions to
>  emboss-dev at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>  http://lists.open-bio.org/mailman/listinfo/emboss-dev
> or, via email, send a message with subject or body 'help' to
>  emboss-dev-request at lists.open-bio.org
>
> You can reach the person managing the list at
>  emboss-dev-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of emboss-dev digest..."
>
>
> Today's Topics:
>
>    1. Anonymous CVS working again :) (Peter)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 7 Sep 2009 12:56:17 +0100
> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: [emboss-dev] Anonymous CVS working again :)
> To: Biopython-Dev Mailing List <biopython-dev at lists.open-bio.org>,
>  emboss-dev at lists.open-bio.org
> Cc: root-l at lists.open-bio.org
> Message-ID:
>  <320fb6e00909070456k28122011o59bfb3d640c4a0a8 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Just an FYI,
>
> While the developer server dev.open-bio.org has been fine, recently
> our public read only mirror at cvs.open-bio.org (and cvs.biopython.org)
> had not been updated. This affected Biopython and EMBOSS.
>
> And for Biopython as a knock on effect, this had meant the latest
> code at http://biopython.org/SRC/biopython/ was a little out of date.
> [Biopython's github mirror was not affected]
>
> These all seem to be working fine once again - thanks to someone
> at the OBF - let me know who and I'll buy you a beer when we (next)
> meet up :)
>
> Peter
>
>
> ------------------------------
>
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>
>
> End of emboss-dev Digest, Vol 13, Issue 1
> *****************************************
>


From biopython at maubp.freeserve.co.uk  Mon Sep  7 20:00:46 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 7 Sep 2009 21:00:46 +0100
Subject: [emboss-dev] [Root-l] Anonymous CVS working again :)
In-Reply-To: <B86883FE-D894-4933-81AE-7D5452075301@illinois.edu>
References: <320fb6e00909070456k28122011o59bfb3d640c4a0a8@mail.gmail.com>
	<B86883FE-D894-4933-81AE-7D5452075301@illinois.edu>
Message-ID: <320fb6e00909071300x6238e828l4440e71c562e792c@mail.gmail.com>

> Are these being kept in sync? ? bioperl's moved completely away from
> cvs to svn with very little pain. ?We found sync-ing the two more trouble
> than it was worth.

Perhaps we are talking at cross purposes here Chris.

Right now Biopython and EMBOSS are using CVS, with developers
committing to dev.open-bio.org, which then updates a read only CVS
mirror code.open-bio.org (aka cvs.open-bio.org aka cvs.biopython.org)
to provide anonymous assess.

Likewise, BioPerl etc are using SVN, with developers committing to
dev.open-bio.org, which then updates a read only SVN mirror at
code.open-bio.org (or its other aliases) to provide anonymous assess.

Peter



From biopython at maubp.freeserve.co.uk  Wed Sep  9 14:30:44 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Sep 2009 15:30:44 +0100
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
Message-ID: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>

Hi all,

I've read the instructions here and have been able to build
the core EMBOSS tools from CVS:
http://emboss.sourceforge.net/developers/cvs.html

However, I would also like to compile the EMBASSY tools,
in particular the PHYLIPNEW suite. Is this procedure
written down?

Thanks,

Peter


From uludag at ebi.ac.uk  Wed Sep  9 14:52:34 2009
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Wed, 09 Sep 2009 15:52:34 +0100
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
In-Reply-To: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
References: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
Message-ID: <1252507954.3070.83.camel@emboss2.ebi.ac.uk>


> I've read the instructions here and have been able to build
> the core EMBOSS tools from CVS:
> http://emboss.sourceforge.net/developers/cvs.html
> 
> However, I would also like to compile the EMBASSY tools,
> in particular the PHYLIPNEW suite. Is this procedure
> written down?

I found the following page by google search which looks relevant.

http://emboss.sourceforge.net/docs/adminguide/node28.html

New EMBOSS documentation have a slightly updated version with an
explanation for the case EMBOSS was not compiled beforehand but it has
not been published in EMBOSS official pages yet.

Regards,
Mahmut




From ajb at ebi.ac.uk  Wed Sep  9 15:18:26 2009
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 9 Sep 2009 16:18:26 +0100 (BST)
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
In-Reply-To: <1252507954.3070.83.camel@emboss2.ebi.ac.uk>
References: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
	<1252507954.3070.83.camel@emboss2.ebi.ac.uk>
Message-ID: <56792.86.26.12.63.1252509506.squirrel@webmail.ebi.ac.uk>

More up-to-date instructions are in the top level FAQ in the
CVS version.

I've just committed a slight fix to that file (it didn't
specify the flags for aclocal and automake - which are as you'd expect)
so it may take a couple of hours to be copied over to the public CVS.
Otherwise the file is pretty much the same as the FAQ from the
distribution.

ATB

Alan


>
>> I've read the instructions here and have been able to build
>> the core EMBOSS tools from CVS:
>> http://emboss.sourceforge.net/developers/cvs.html
>>
>> However, I would also like to compile the EMBASSY tools,
>> in particular the PHYLIPNEW suite. Is this procedure
>> written down?
>
> I found the following page by google search which looks relevant.
>
> http://emboss.sourceforge.net/docs/adminguide/node28.html
>
> New EMBOSS documentation have a slightly updated version with an
> explanation for the case EMBOSS was not compiled beforehand but it has
> not been published in EMBOSS official pages yet.
>
> Regards,
> Mahmut
>
>
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>




From biopython at maubp.freeserve.co.uk  Wed Sep  9 15:34:06 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Sep 2009 16:34:06 +0100
Subject: [emboss-dev] Compiling EMBASSY packages from CVS
In-Reply-To: <4AA7C0CD.7020403@ebi.ac.uk>
References: <320fb6e00909090730g2425fef8q45206371389b7bc7@mail.gmail.com>
	<4AA7C0CD.7020403@ebi.ac.uk>
Message-ID: <320fb6e00909090834w49dd3e53xee1a4d9f14770fdd@mail.gmail.com>

On Wed, Sep 9, 2009 at 3:50 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
>
> The installation is the same as for EMBOSS. You just need to cd to
> embassy/packagename
>
> cd embassy
> cd phylipnew
> aclocal -I m4
> autoconf
> automake -a
> ./configure (same options as you used for EMBOSS)
> make
> make install

Thanks.

I had tried that but there was a build problem, probably related to
my not yet having updated libtool on this machine.

So there is nothing like make-static-developers?

Peter C


From jbdundas at gmail.com  Sun Sep 13 11:13:22 2009
From: jbdundas at gmail.com (jitesh dundas)
Date: Sun, 13 Sep 2009 16:43:22 +0530
Subject: [emboss-dev] Can I help.
Message-ID: <326ea8620909130413x79c01f29g70280bc59dec7cda@mail.gmail.com>

Dear Sir/Madam,

I would like to contribute to this project. Is  there anything that I could
do to help..

Please let me know if you need anything else from my side..

Regards,
Jitesh Dundas


From biopython at maubp.freeserve.co.uk  Wed Sep 16 23:23:37 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Sep 2009 00:23:37 +0100
Subject: [emboss-dev] PHYLIP(NEW) and stdout
In-Reply-To: <320fb6e00909161614r288fb399o22328bbb4f4de230@mail.gmail.com>
References: <320fb6e00909161614r288fb399o22328bbb4f4de230@mail.gmail.com>
Message-ID: <320fb6e00909161623u4d4f2eb6s5dedb61b28308f74@mail.gmail.com>

Hi all,

Some years ago I filed bug 1587853 about fseqboot including "noisy"
output on stdout, which means it can't be used for bootstrapping where
the resampled alignments are sent to stdout (e.g. using the -filter or
-stdout arguments). e.g.

cat tiny.phy | fseqboot -reps 3 -filter

I've just found fdnadist has the same problem, in addition to the
distance matrices (the actual output) progress messages are also
printed to stdout (when using the -filter or -stdout arguments). e.g.

cat opuntia.fasta | fdnadist -method k -filter
fdnadist -sequence opuntia.fasta -method k -stdout -auto
fdnadist -sequence opuntia.fasta -method k -filter

I presume this is symptomatic of all the PHYLIPNEW tools, which is a
shame as it prevents piping their output together which to me is the
natural way to use these tools (rather than messing about with named
temporary files). It also spoils my plans for calling the PHYLIP tools
from Python and capturing their output via stdout (again, without
messing about with temp output files).

Would it be simple to make all these progress messages go to stderr
instead of stdout? Or just disable them if -stdout or -filter has been
used? I can appreciate that as you are wrapping a 3rd party tool here,
any EMBOSS specific changes should be kept to a minimum, so this
may not be that simple.

If no one other than me has asked about this, perhaps it isn't a big
issue for most EMBOSS+PHYLIP users?

Regards,

Peter C.


From pmr at ebi.ac.uk  Thu Sep 17 00:22:39 2009
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 17 Sep 2009 01:22:39 +0100
Subject: [emboss-dev] PHYLIP(NEW) and stdout
In-Reply-To: <320fb6e00909161623u4d4f2eb6s5dedb61b28308f74@mail.gmail.com>
References: <320fb6e00909161614r288fb399o22328bbb4f4de230@mail.gmail.com>
	<320fb6e00909161623u4d4f2eb6s5dedb61b28308f74@mail.gmail.com>
Message-ID: <4AB1814F.6060207@ebi.ac.uk>

Peter C. wrote:
> Hi all,
> 
> Some years ago I filed bug 1587853 about fseqboot including "noisy"
> output on stdout, which means it can't be used for bootstrapping where
> the resampled alignments are sent to stdout (e.g. using the -filter or
> -stdout arguments). e.g.
>
> Would it be simple to make all these progress messages go to stderr
> instead of stdout? Or just disable them if -stdout or -filter has been
> used? I can appreciate that as you are wrapping a 3rd party tool here,
> any EMBOSS specific changes should be kept to a minimum, so this
> may not be that simple.

Yes ... the phylip code is pretty clean and we could put something in to 
catch these messages with stdout as the default but some other output 
available as a command line option.

I just added the phylip 3.69 code changes in CVS. I will look into this 
when I am back next week.

regards,

Peter


From ajb at ebi.ac.uk  Wed Sep 23 11:17:06 2009
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 23 Sep 2009 12:17:06 +0100 (BST)
Subject: [emboss-dev] Major changes to AJAX structure in CVS
Message-ID: <43251.86.26.12.63.1253704626.squirrel@webmail.ebi.ac.uk>

Dear developers,

Major structural work has been done on the structure
of AJAX on the CVS server this morning. This is associated
with a future intention to move ACD functions into
a separate library. This will allow it to call sub-libraries
which will perform various new methods of data retrieval without
having to incorporate all those methods into one monolithic
libajax library.


As of today AJAX has the following subdirectories:

  pcre core graphics ensembl ajaxseq acd

pcre: file in here are the ones from the original ajax directory
      and compile to create a libepcre library.

core: currently contains all the aj*.c/h files from the original
      ajax directory with the exception of the graphics
      C files (some headers are left for the moment to
      avoid circular dependencies until ACD functions are moved).
      These files create a libajax library as before.

graphics: contains the ajgraph* and ajhist* files and, as before,
      create a libajaxg library

ensembl: New routines for accessing Ensembl. A work in progress.
      They create a libensembl library.

ajaxseq: A placeholder for ajax sequence handling source to be
     moved from core as part of the ACD changes. Currently
     this contains dummy source files and creates a
     libajaxseq library.

acd: A placeholder or the ACD functions to be moved. Currently this
     contains dummy source files and creates a libacd library.


These changes have, of course, required significant changes to
Makefile.am files thoughout EMBOSS and EMBASSY.


Given the major changes involved I'd recommend using a fresh
checkout of EMBOSS as you may have problems with
a "cvs update -dP" - old dependencies (etc) may still
exist in hidden directories (.libs/.deps/etc) which
could potentially mess things up. You should certainly
try a fresh checkout before emailing with related problems.


If you use the myemboss development area then the configuration for
that has been updated. If, however, you've made your own EMBASSY-style
packages then you'll need to modify your configuration using
one of the new Makefile.am files as a template.


A further change has been to add preliminary ajsql.c/h files
to AJAX. This has involved adding checks for MYSQL and POSTGRESQL
in the top level configuration (and two new m4 files in the m4
directory).

The configuration and compilation should be happy whether you have
both SQL development files installed, only one or none. However,
if you experience any problems in the compilation
in that area then please let me know.

The changes may take a couple of hours to propagate to the
anonymous CVS server.

Alan