Re: [Seqan-dev] Fwd: having problem in including seqan library to dev c++

[Nazish Jamil <nzshjamil@yahoo.com>]

Dear Rahn, René,

Thanks for your help,but some steps i cant understand....anyways can u suggest me efficient algorithm for MPSA software ????

 and i still follow your steps for including seqAn library in eclipse 

  Thanks

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From: "Rahn, René" <rene.maerker@fu-berlin.de>
To: Nazish Jamil <nzshjamil@yahoo.com>
Cc: SeqAn Development <seqan-dev@lists.fu-berlin.de>
Sent: Thursday, February 28, 2013 8:33 PM
Subject: Fwd: [Seqan-dev] having problem in including seqan library to dev c++

Dear Nazish,

1. Install MinGW by following the installation instructions here: http://www.mingw.org/wiki/Getting_Started. 

2. Make sure you have no parallel cygwin installation, because cmake does not allow any sh.exe in the PATH environment. (Is still an open issue in cmake)!

 Anyway if you really need cygwin installation use the path fix batch file in "util/mingw/mingw_path_fix" to temporarily remove the cygwin path from within the terminal session you are currently in. It is important to start eclipse from within this terminal session, so that the PATH is fixed for this session. This is a little workaround we added for MinGW/Cygwin user. Note, that cygwin is at the moment not supported as a build system within the windows environment. Regardless of this, you should be able to run with native cygwin compilers within a cygwin bash. But than you also could just run a linux :).

3. Download the latest eclipse build from their homepage. Note, that there are known issues with the 64 bit version of eclipse regarding the console output (it is slow :) ). But this will be probably fixed by the next major release of CDT?!  If you have installed eclipse-cdt than you just need to add the svn plugin within eclipse. 

Go to help-> install new software -> select update site of your eclipse build (probably indigo). In the Dialog box below search for svn and check  Subversive SVN Team Provider (Incubation). Confirm all questions and wait for install to be finished. 

Restart eclipse as prompted and go to project view 'svn repository exploring'. Wait for install to be finished and restart eclipse. Add a new resource (fill in the svn trunk address of seqan) within the svn repository perspective. Checkout Seqan trunk. Wait until it is finished.

4. From here on you just can follow the steps described here: http://trac.seqan.de/wiki/Tutorial/GettingStarted/LinuxEclipse#AFirstBuild

These steps are only necessary if you plan to work within SeqAn. However,if you have your own project and you want to just use our library, then you only have to link against the seqan library. How you can do that is described here: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem

Try these steps and let me know if it worked out.

Kind regards,

René

Begin forwarded message:

From: Nazish Jamil <nzshjamil@yahoo.com>

Subject: Re: [Seqan-dev] having problem in including seqan library to dev c++

Date: February 28, 2013 3:57:28 PM GMT+01:00

To: Rahn, René <rene.maerker@fu-berlin.de>, "SeqAn Development" <seqan-dev@lists.fu-berlin.de>

Reply-To: Nazish Jamil <nzshjamil@yahoo.com>

Dear Rahn, René

Thank you so much and so nice of you that you help me. ok ,i am using windows...i also tried eclipse but i dont understand....ok if i again install eclipse how can i include seqan ????im interseted in using c/c++IDE.

thanks

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From: "Rahn, René" <rene.maerker@fu-berlin.de>
To: Nazish Jamil <nzshjamil@yahoo.com>; SeqAn Development <seqan-dev@lists.fu-berlin.de>
Sent: Thursday, February 28, 2013 7:46 PM
Subject: Re: [Seqan-dev] having problem in including seqan library to dev c++

Dear Nazish,

I also tried Dev c++ once, but couldn't find appropriate support within the cmake system for this IDE so I let it go. As far as I remember KDevelop seems to work and if you are working on a windows machine, we strongly recommend to use visual studio (the express version is free of charge). If you are working on a mac os, we recommend to use Xcode. Personally, I work with Eclipse which runs smooth on all systems as long as you have enough RAM (minimum should be 4 GB).

You can find more support on the website: http://trac.seqan.de/wiki/Tutorial/GettingStarted.

Note, that eclipse on windows works just fine but is a little bit more complicated to set up.

On the wiki page linked above you'll also find some instructions of how to bind our library in to your project, so you can use your own build system if you want.

Please, let us know if we can be of any more help.

Kind regards,

René Rahn

On Feb 28, 2013, at 3:26 PM, Nazish Jamil wrote:

hello,i have problem when including seqAn library to Dev c++ ???please help me in including this library??? actually our project is designing software for MPSA(multiple protein sequence alignment)...thatswhy we are intersted in using seqan library????you have any solution for this problem or suggest any other IDE for seqan 

 thanks 

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René Rahn

Ph.D. Student

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rene.rahn@fu-berlin.de

+49 (0)30 838 75 277

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Algorithmic Bioinformatics (ABI)

Department of Informatics 

Room  018

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Freie Universität Berlin

Takustraße 9 

14195 Berlin

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---

René Rahn

Ph.D. Student

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

rene.rahn@fu-berlin.de

+49 (0)30 838 75 277

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

Algorithmic Bioinformatics (ABI)

Department of Informatics 

Room  018

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

Freie Universität Berlin

Takustraße 9 

14195 Berlin

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