Re: [Seqan-dev] installing Mason

[Rahn, René <Rene.Rahn@fu-berlin.de>]

Hi Elizabeth,

thanks for reaching out to us.

On 13. Sep 2019, at 16:43, Elizabeth Yuu <yuue@zedat.fu-berlin.de> wrote:

To whom this may concern,

I'm a PhD student at the Robert Koch Institute and I am trying to simulate
reads using Mason. I have downloaded the .zip file and I see that I must
apply the following steps svn co
http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk cd
seqan-trunk/build
   mkdir Release
   cd Release
   cmake -DCMAKE_BUILD_TYPE=Release ..
   make mason
./core/apps/mason/mason --help

These are all very old links. In the meantime mason was updated to mason2 and can the sources can be obtained via GitHub: https://github.com/seqan/seqan. There you can clone the repository and build the mason2 app from source. A general documentation can be found here: https://seqan.readthedocs.io/en/master/Infrastructure/Use/index.html. Or you just download the latest binary form http://packages.seqan.de/mason2/

I also tried using the link
http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted

I cannot access either of the two links. Is there another way to install
mason/ a tutorial?

Second, I am trying to reproduce results of a paper and I see the paper
uses Mason in two ways to produce Illumina reads. For example, I see "
mason_simualtor --illumina -n 100 ...." and then in another part I see
"masson illumina -n 100 ..." . what is the difference between these two
commands?

Not sure. Maybe a wrong command? If they are using mason and not mason2 then this can be quite old too. I am afraid I can't help you with this then.

Best regards,

René Rahn

Many thanks in advance.
Best,
Elizabeth

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---

René Rahn

Ph.D. Student (de.NBI - CIBI)

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Tel:  (+49) 30 838 72974

Mail: rene.rahn@fu-berlin.de

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Institute of Computer Science

Algorithmic Bioinformatics (ABI)

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Freie Universität Berlin

Takustraße 9

14195 Berlin

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