Question: installing bwa for linux 32 bits
0
gravatar for cvjuanjo87
7 months ago by
cvjuanjo8710
cvjuanjo8710 wrote:

Hi, I'm new in linux usage. I'm trying to install bwa (0.5.7; 0.5.9; 0.5.10; 0.7.x versions) but i get an error. I get 'is missing for channels 32' when i tried to install by conda. I think the problem would be because my machine is 32 bits. then, I need help to continue my learnig. I would like to know if there is another way to install bwa or if there is another compatible version of bwa for linux 32 bits.

I hope what I have requested is possible.

bwa software error • 501 views
ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 7 months ago by cvjuanjo8710
1

see Installing Bwa On 32 Bit Unix Machine

ADD REPLYlink written 7 months ago by Pierre Lindenbaum108k

What is the OS you're running? What's the reason for using conda for install? What is the output of uname -a in the terminal?

ADD REPLYlink modified 7 months ago • written 7 months ago by st.ph.n2.2k
1

I don't think people need to legitimize using conda, it's kind of the standard for installing bioinformatics software.

ADD REPLYlink written 7 months ago by Devon Ryan80k

The output of uname -a is: Linux 4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:34:49 UTC 2016 i686 i686 i686 GNU/Linux.

ADD REPLYlink written 7 months ago by cvjuanjo8710
1

install bwa via synaptic in ubuntu.

ADD REPLYlink written 7 months ago by cpad01126.3k

compiled version

https://github.com/lh3/bwa/tree/master/bwakit

Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping. In addition to the basic mapping functionality implemented in bwa, bwakit is able to generate proper human reference genome and to take advantage of ALT contigs, if present, to improve read mapping and to perform HLA typing for high-coverage human data. It can remap name- or coordinate-sorted BAM with read group and barcode information retained.

ADD REPLYlink modified 7 months ago • written 7 months ago by Medhat7.6k

do you need all the versions mentioned in OP? If you are on ubuntu or debian or mint, sudo apt-get install bwa -y will install current version of bwa (in repos) on your machine

ADD REPLYlink modified 7 months ago • written 7 months ago by cpad01126.3k

If you are using (or have a human genome sized genome) then 32-bit is not going to cut it.

ADD REPLYlink written 7 months ago by genomax49k

I want to use it for smaller genomes (bacterial genomes)

ADD REPLYlink written 7 months ago by cvjuanjo8710

Try precompiled version.

ADD REPLYlink written 7 months ago by arup340
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