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Old 08-28-2013, 05:26 AM   #1
felipelira3
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Exclamation Uninstall MIRA assembler

I am trying to install the new version of MIRA 4 but I think that itś necessary to uninstall the oldest version.

Does anyone can help me with it?

Thank you
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Old 08-28-2013, 07:26 AM   #2
SES
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I don't think this would be necessary. The program names have not changed (to my knowledge), and installing should just replace the old binaries. You can just compile mira and use it in place, or install it and that should give you the latest version in your path.
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Old 08-28-2013, 07:34 AM   #3
felipelira3
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Default problem almost solved

Now it reclains the TCmalloc library.
I tried to do what recommends the MIRA manual, but didn works:

sudo apt-get install make flex libgoogle-perftools-dev
sudo apt-get install libboost-doc libboost.*1.48-dev libboost.*1.48.0

Any suggestion?
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Old 08-28-2013, 07:47 AM   #4
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You will have to clarify what you mean by "didn't work." It looks like you are trying to install dependencies for mira, so I'm guessing you had troubles with installation. What exactly are the issues you are experiencing, and what are the messages you see?
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Old 08-28-2013, 07:55 AM   #5
felipelira3
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Yes, I have a problem. I saw that the MIRA installed before was installed by Ubuntu Software Center. It made it easier. I uninstalled it and now I'm having some problems with the new version.

The message that appears after "./configure" is:

"Could not find the tcmalloc library. It is part of the Google perftools library at
http://code.google.com/p/google-perftools/downloads/list"

I looked for this files and I saw that they are installed.
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Old 08-28-2013, 07:56 AM   #6
GenoMax
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Quote:
Originally Posted by felipelira3 View Post
Now it reclains the TCmalloc library.
I tried to do what recommends the MIRA manual, but didn works:

sudo apt-get install make flex libgoogle-perftools-dev
sudo apt-get install libboost-doc libboost.*1.48-dev libboost.*1.48.0

Any suggestion?
Are you referring to missing libtcmalloc? You should be able to get that from libtcmalloc-minimal4 perhaps (or libgoogle-perftools-dev).
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Old 08-28-2013, 08:06 AM   #7
felipelira3
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Quote:
Originally Posted by GenoMax View Post
Are you referring to missing libtcmalloc? You should be able to get that from libtcmalloc-minimal4 perhaps (or libgoogle-perftools-dev).
It would be installed unsing "sudo apt-get install make flex libgoogle-perftools-dev", doesn it?
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Old 08-28-2013, 08:10 AM   #8
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Following should be enough I think.

Quote:
Originally Posted by felipelira3 View Post
"sudo apt-get install libgoogle-perftools-dev"
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Old 08-28-2013, 09:03 AM   #9
felipelira3
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Hi GenoMax

I will try to follow all the steps from the begin, since download the file mira-4.0rc1.tar.bz2.
If I have any problem, I'll describe it here.

Thank you a lot!
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Old 08-30-2013, 03:07 AM   #10
sklages
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Any reason why you don't want to use the precompiled binaries? This is usually easier (especially if your are not an expert compiling software on your own).
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Old 08-30-2013, 03:13 AM   #11
felipelira3
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Quote:
Originally Posted by sklages View Post
Any reason why you don't want to use the precompiled binaries? This is usually easier (especially if your are not an expert compiling software on your own).
It will be my last alternative. I am trying to learn how to compile it. Thank you!
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Old 09-02-2013, 01:46 PM   #12
felipelira3
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Thank you for your attention about helping me with the mira4 installation. But now I have a doubt.

How can I insert the parameter at the manifest to avoid the large sequence names with more then 40 letters and ignore it to follow the assembly steps?
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Old 09-04-2013, 01:32 PM   #13
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Why don't you read the manual? Have a look at it and search for "check_maxreadnamelength".
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Old 09-04-2013, 11:49 PM   #14
felipelira3
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Default Thank you

Quote:
Originally Posted by sklages View Post
Why don't you read the manual? Have a look at it and search for "check_maxreadnamelength".
I solved the problem by myself but didn have time to put it here. Thank you for your attention.

The problem was because I was using the SOLEXA_SETTINGS instead the COMMON_SETTINGS to skip the reads name length. My alternative was:

project = assembly_bs10_3
job = genome,denovo,accurate
parameters = COMMON_SETTINGS -NW:cmrnl=no

But, if you have another alternative to this, we wil be too glad if you share it with us...

Have a good day
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Old 09-05-2013, 12:01 AM   #15
sklages
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No alternative. Makes sense that "check_maxreadnamelength/maxreadnamelength" is COMMON_SETTINGS as it is technology-independent. Downstream programs may run into problems with very long readnames, no matter which technology.
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