[mira_talk] Re: help with mapping assembly for ion torrent data
- From: Sebastian Juenemann <jueneman@xxxxxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 28 May 2013 10:27:40 +0200
On 05/28/13 04:42, Austen Chen wrote:
Thanks Bastien, and you must think what the hell you still use that old
version; well I maybe dumb in terms of bioinformatics (as a biologist
trying to embark on this new field) but not that dumb when a new and
better version is available. The problem is that our linux server uses
an old gcc version and doesn't allow installation of new mira versions.
When I asked them to install 3.9.15 and that's what happened:
Updating gcc will break some other stuff on the server, so I can not do
it. I have backed mira down to 3.4.1.1, and will continue to look into a
solution. Sorry I can't do the upgrade at this point.
This sounds wired, anyhow i assume you're struggling with your system
administration at this particular point?
Two things worth to consider:
1) Albeit i do not recommend this but of course you can have several
parallel installations different GCC versions. If you're not using a
very exotic OS then maybe you could try and install a local recent GCC
version.
2) If it's possible to use a virtual Box or alike on your system then
this might also be a intermediate solution.
That's why I tried to install it on my mac but ran into a problem with
gcc compiler (if you can recall that I have sent you a mail regarding
this) and you suggested not to use Mac.
It has not been a smooth ride for me on the mira, and I should have
consulted the new manual as I only had a quick look on the new one and
thought it's not much different from the 3.4.0 which I have printed out.
Well enough a long story, basically there is no way that I can do
mapping assembly unless I got the new version running?
Sorry for all these dumb questions and that's why you are here to help?
Much appreciated
Austen
From: Bastien Chevreux <bach@xxxxxxxxxxxx <mailto:bach@xxxxxxxxxxxx>>
Reply-To: "mira_talk@xxxxxxxxxxxxx <mailto:mira_talk@xxxxxxxxxxxxx>"
<mira_talk@xxxxxxxxxxxxx <mailto:mira_talk@xxxxxxxxxxxxx>>
Date: Tuesday, 28 May 2013 1:20 AM
To: "mira_talk@xxxxxxxxxxxxx <mailto:mira_talk@xxxxxxxxxxxxx>"
<mira_talk@xxxxxxxxxxxxx <mailto:mira_talk@xxxxxxxxxxxxx>>
Subject: [mira_talk] Re: help with mapping assembly for ion torrent data
On May 27, 2013, at 12:15 , Austen Chen <austen.chen@xxxxxxxxxxxxxxx
<mailto:austen.chen@xxxxxxxxxxxxxxx>> wrote:
The version I used was v3.4.1.1
Do yourself a favour and take the latest development version for Ion data:
http://sourceforge.net/projects/mira-assembler/files/MIRA/development/
Docs in the package or online here:
http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html
Please read up the four or five sections on how to write manifest files
http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html#sect_ref_config
and here's a simple example for a mapping assembly with Illumina data
(you'll be able to find out how to change file formats and technology
used, I'm sure):
http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html#sect_sxa_ma_writing_a_simple_manifest_file
B.
--
Sebastian Jünemann
CeBiTec - Center for Biotechnology
Bielefeld University, D-33594 Bielefeld, Germany
Office: V6-147 -- Phone: +49-(0)521-106-4827
eMail: jueneman@xxxxxxxxxxxxxxxxxxxxxxxx
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