Re: [AMOS-devel] AMOS release *Update*

[Florent A. <flo...@gm...>]

Hi all,

I am CC'ing this email to amo...@li... since it is 
related to the development of AMOS. We should probably use this email 
address more often to keep in touch...

While it is truly excellent that there is a new version of AMOS, I found 
some issues with the released package (and some more general AMOS 
issues). I would have liked to have the opportunity to look at the 
package before its release so that these issues could have been fixed.

1/ There was a missing file (Utilities_Bundler.hh) but this is fixed now.

2/ The AMOS version number was not updated for this release. It should 
be changed to 3.0.0 in the file configure.ac

3/ The changelog file (called 'NEWS') has not been updated since 2.0.5. 
With a major version release, I would have expected it to be up-to-date, 
especially when an email was sent previously to the developers to gather 
this information.

4/ I still get warnings when installing AMOS. I can try to fix them, but 
before I do, does anyone know already exactly how to fix them?
Deprecated warnings:
In file included from 
/usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/ext/hash_map:60,
                  from ../../../src/AMOS/utility_AMOS.hh:38,
                  from ../../../src/AMOS/foundation_AMOS.hh:13,
                  from clk.cc:15:
/usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/backward/backward_warning.h:28:2: 
warning: #warning This file includes at least one deprecated or 
antiquated header which may be removed without further notice at a 
future date. Please use a non-deprecated interface with equivalent 
functionality instead. For a listing of replacement headers and 
interfaces, consult the file backward_warning.h. To disable this warning 
use -Wno-deprecated.

5/ I've noticed that there are 2 apparently redundant folders in the 
main CVS repository: 'bankviewer' and 'hawkeye'. Shall we remove one or 
the other?

6/ I'd like to test some of the new features of AMOS. Yet, even as a 
developer, I am unsure where to find them. For example, where is 
fast2amos or goBambus2?

7/ At some point, Figaro was supposed to be integrated into the main 
AMOS repository. This has not yet been done, and I'll probably do it 
myself unless there are reasons not to.

8/ Recently, there were some emails on the mailing list from Martin 
Mokrejs (mmo...@fo...). He reported many issues related 
to compiling, but got very little feedback from us. Hopefully, we can 
address some of his points so that he didn't feel like he entirely 
wasted his time trying to help the AMOS project.

Looking forward to hearing your thoughts about it all. Best,

Florent



On 19/11/10 22:18, Mihai Pop wrote:
> Florent,
>
> Dan and Todd have been testing the code and found a few bugs that they are fixing now.
>
> Mihai
>
> "Florent Angly"<flo...@gm...>  wrote:
>
>> I'm interested in the answer to this question too. Thanks!
>> Florent
>>
>> On 16/11/10 08:14, Michael Schatz wrote:
>>> Hi Dan,
>>>
>>> How is the release going? Also, where is the source code for
>>> fast2amos. I don't see it in the CVS.
>>>
>>> Thanks,
>>>
>>> Mike
>>>
>>>
>>> On Fri, Oct 29, 2010 at 8:29 AM, Daniel Sommer
>> <ds...@um...
>>> <mailto:ds...@um...>>  wrote:
>>>
>>>      Guys,  The release date has been moved back one week so that some
>>>      changes can be made to Bambus 2.0.  The new release date will be
>>>      Nov. 8.
>>>
>>>      -Dan
>>>
>>>
>>>      On Sun, Oct 24, 2010 at 5:19 PM, Michael Schatz
>>>      <ms...@um...<mailto:ms...@um...>>  wrote:
>>>
>>>          Here are a few more highlights:
>>>
>>>          * bank2contig - support for writing SAM format
>>>          * libSlice - correctly compute consensus even with very deep
>>>          coverage
>>>          * Hawkeye - experimental support for Qt 4
>>>          * genome-complexity - Compute the complexity of a genome (See
>>>          http://www.biomedcentral.com/1471-2105/11/21)
>>>          * many small updates and bug fixes
>>>
>>>          Full Changelog attached.
>>>
>>>          Mike
>>>
>>>
>>>
>>>          On Fri, Oct 22, 2010 at 8:34 PM, Florent Angly
>>>          <flo...@gm...<mailto:flo...@gm...>>
>> wrote:
>>>              Agreed. Excellent!
>>>              Other things to add to the changelog:
>>>                  * many little fixes in the Perl converters
>>>                  * Minimo - the minimus assembler with many more
>> options
>>>              Florent
>>>
>>>
>>>
>>>              On 23/10/10 09:25, Adam Phillippy wrote:
>>>>              Awesome. Thanks Dan. A new release is long overdue!
>>>>
>>>>              Sent from my iPhone.
>>>>
>>>>              On Oct 22, 2010, at 6:30 PM, Dan Sommer
>>>>              <ds...@um...<mailto:ds...@um...>>
>>>>              wrote:
>>>>
>>>>>              Guys,  We are planning on doing an official AMOS
>> release
>>>>>              on Tuesday Nov. 2.  Let me know if that date doesn't
>>>>>              work for you.  If you have anything you would like to
>> be
>>>>>              included in the release please have the code checked in
>>>>>              by Nov 1 and send me a description that can be included
>>>>>              in the release notes.  Currently the changes for this
>>>>>              release will include the following:
>>>>>
>>>>>                  * Bambus 2.0 -  new scaffolder developed by Sergey
>>>>>                  * fast2amos - utility that can convert large fastq
>>>>>                    files into a bank
>>>>>                  * Autoconf -  the ability to build only core AMOS
>>>>>                    binaries
>>>>>                  * Unitigger - Updated unitigger for minimus
>>>>>
>>>>>
>>>>>              Let me know if I am missing anything or you need to set
>>>>>              a different date.
>>>>>
>>>>>              Dan
>>>>>
>>>
>>>
>>>