Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8

Kathrin Trappe <kathrin.trappe@fu-berlin.de> · Thu, 31 May 2012 09:56:33 +0200

lol :)

On 05/31/2012 09:52 AM, Singer, Jochen wrote:

Hi all,

sorry for my stupidity. Just ignore the last mail!

Sorry for the inconvenience,
Jochen

On 31.05.2012, at 09:48, Singer, Jochen wrote:

Hi Manuel,

ich wollte dich nur fragen, ob ihr mir bescheid sagen könnte, wenn ihr euch für code entscheidet, da ich so auch sehe, welche teile sensibel sind :-)

On 31.05.2012, at 08:47, Holtgrewe, Manuel wrote:

Hi Neal, sorry for providing the HTTPS link. The correct link is:

http://trac.seqan.de/wiki/HowTo/InstallContribsWindows

The SeqAn Trac is publically available via HTTP.

I'll send another email about performance sensitive code later after a discussion with colleagues.

Cheers,
Manuel
________________________________________
From: Neil Justice [njjustice@gmail.com]
Sent: Thursday, May 31, 2012 6:12 AM
To: seqan-dev@lists.fu-berlin.de
Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8

Thanks Manuel. Your fix to that CMakeLists.txt file allowed me to run
CMake without error and generate an .sln file.

The code now builds for me except for these four compiler errors:

error C3861: 'Bam': identifier not
found   c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp  244
error C2665: 'open' : none of the 8 overloads could convert all the
argument types  c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp  238
error C2079: 'inBamStream' uses undefined class
'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp  237
error C2065: 'Bgzf' : undeclared
identifier      c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp  237

How are these errors resolved?

Assuming these errors are resolved by obtaining zlib/bzlib: link
https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a
login/password prompt for FU Berlin for which I have no login or
password. Is there another link to zlib/bzlib?

Also, which files contain the most performance-sensitive code?

Cheers,
Neil

On Tue, May 29, 2012 at 5:00 AM,<seqan-dev-request@lists.fu-berlin.de>  wrote:

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Today's Topics:

1. Re: I'm interested in making SeqAn faster but am stopped by
    these CMake errors (Holtgrewe, Manuel)

----------------------------------------------------------------------

Message: 1
Date: Mon, 28 May 2012 10:14:43 +0000
From: "Holtgrewe, Manuel"<manuel.holtgrewe@fu-berlin.de>
To: SeqAn Development<seqan-dev@lists.fu-berlin.de>
Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am
      stopped by      these CMake errors
Message-ID:
      <FCCAB9D80C3DAB47B5601C5B0E62872B0949E1@ex02a.campus.fu-berlin.de>
Content-Type: text/plain; charset="us-ascii"

Dear Neil,

the problem is caused by a bug in one of the CMakeLists.txt files. This should be corrected now.

As for zlib/bzlib, you can simply install prebuilt versions of these libraries:

https://trac.seqan.de/wiki/HowTo/InstallContribsWindows

Most of the library will also work without zlib, but for reading BAM files or compressed streams, you will need it. This is also explained in some detail in some messages after the configuration.

Cheers,
Manuel
________________________________________
From: Neil Justice [njjustice@gmail.com]
Sent: Monday, May 28, 2012 2:32 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopped by    these CMake errors

Hello SeqAn developers,

My name is Neil Justice and I'm interested in helping advance genetics
research by contributing my programming skills to the task of making
SeqAn faster. I work on performance tuning the C++ of a high-frequency
algorithmic trading program at a hedge fund in Houston. Lately I've
been interested in finding an interesting and good-for-humanity open
source project to work on at home, and SeqAn appears to be that
project.

I am on Windows and am trying to generate a Visual Studio 2008 .sln
for SeqAn using CMake. I've pulled the code using svn per tutorial
http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake
errors I encounter in response to CMake command "cmake
C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached
as a screenshot):

PS C:\Seqan\build>  cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"
-- Check for working C compiler using: Visual Studio 9 2008
-- Check for working C compiler using: Visual Studio 9 2008 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler using: Visual Studio 9 2008
-- Check for working CXX compiler using: Visual Studio 9 2008 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
SEQAN_CONTRIB_BASE is undefined!
-- CMAKE_FIND_ROOT_PATH is "".
-- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3")
-- Zlib could not be found!
-- BZip2 libraries could not be found!
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY
-- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed
-- Performing Test TR1_SHARED_PTR_USE_MEMORY
-- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success
-- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP
-- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed
-- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP
-- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success
-- Could NOT find Boost
-- Looking for include file execinfo.h
-- Looking for include file execinfo.h - not found.
-- INFO: Rabema not build because zlib was not found.
CMake Error at core/apps/rabema/CMakeLists.txt:43 (install):
install TARGETS given target "rabema_build_gold_standard" which does not
exist in this directory.

-- Boost not found, not building snp_store.
-- Configuring incomplete, errors occurred!
PS C:\Seqan\build>
PS C:\Seqan\build>

How would you fix these errors? I don't have Zlib or BZip2 (do I need
to download these libraries?). I have Boost (which was not found - do
I need to specify its path somewhere?). I have Python (which was
found).

Thanks and I look forward to finding some SeqAn performance issues.

Neil

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