NGS BWA Installing

Question

[gowdamonish17]

i am unable to install bwa in linux when ever i command "sudo apt-get install bwa" its not installing and its showing "unable to locate package bwa" please help me solve this ASAP

[Rob]

You should try google ASAP.

Without joke, bwa and a lot of bioinformatics tools are not in the linux core library, that's why you can't install them with apt. For install a tool which is not in those library you have to download the package directly from the tool's website and follow instructions.

[gowdamonish17]

thank u for your reply but after commanding " tar -xvf bwa-0.7.12.tar.bz2" im getting " tar: bwa-0.7.12.tar.bz2: Cannot open: No such file or directory tar: Error is not recoverable: Exiting now" this is being displayed. i downloaded the bwa-0.7.12.tar.bz2 which was a latest version available.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWERS is only for new answers for original question.

[GenoMax]

Use tar -xvjf bwa-0.7.12.tar.bz2

[gbl1]

Hi,

I dig it up for I have a small issue.

I tried to install but…

dsl-hkibng42-5673d7-72:bwa-0.7.17 benjamin$ ./configure
-bash: ./configure: No such file or directory

I looked, there is no "autogen.sh" but there is a makefile

dsl-hkibng42-5673d7-72:bwa-0.7.17 benjamin$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kthread.c -o kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kstring.c -o kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt.c -o bwt.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bntseq.c -o bntseq.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwa.c -o bwa.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem.c -o bwamem.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_pair.c -o bwamem_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_extra.c -o bwamem_extra.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  malloc_wrap.c -o malloc_wrap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  QSufSort.c -o QSufSort.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_gen.c -o bwt_gen.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  rope.c -o rope.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  rle.c -o rle.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtindex.c -o bwtindex.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwashm.c -o bwashm.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwase.c -o bwase.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtgap.c -o bwtgap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtaln.c -o bwtaln.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bamlite.c -o bamlite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwape.c -o bwape.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kopen.c -o kopen.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  pemerge.c -o pemerge.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  maxk.c -o maxk.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  fastmap.c -o fastmap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  main.c -o main.o
gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread

Then install failed.

[ATpoint]

So what is the error? Didn't it find libz?

[gbl1]

error is:

dsl-hkibng42-5673d7-72:bwa-0.7.17 benjamin$ install usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode] [-o owner] file1 file2 install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode] [-o owner] file1 ... fileN directory install -d [-v] [-g group] [-m mode] [-o owner] directory ...

which libz does not find anything

Answer 1

[WouterDeCoster]

Installation from bioconda is often the easiest. Install the conda package manager, configure channels (https://bioconda.github.io/index.html#set-up-channels )

and then it's as easy as conda install bwa.

This works for most commonly used tools and will save you a lot of headaches.

Answer 2

[Medhat]

https://sourceforge.net/projects/bio-bwa/

 tar -xvf bwa-x.x.x.tar.bz2   
 cd bwa-x.x.x

 ./configure  
 make  
 make install

http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial

Note: the bwa package exist for this distribution

• precise (12.04LTS) (science): Burrows-Wheeler Aligner [universe]
  0.6.1-1: amd64 armhf i386 powerpc
• trusty (14.04LTS) (science): Burrows-Wheeler Aligner [universe]
  0.7.5a-2: amd64
• xenial (16.04LTS) (science): Burrows-Wheeler Aligner [universe]
  0.7.12-5: amd64
• yakkety (science): Burrows-Wheeler Aligner [universe]
  0.7.15-2: amd64

to find your release

cat /etc/*-release

http://packages.ubuntu.com/search?keywords=bwa&searchon=names&exact=1&suite=all§ion=all

Answer 3

[chen]

If you want to install it via apt-get, try sudo apt-get update first.

Otherwise, you can download the source, and compile it

Answer 4

[giri.ganesh337]

sudo apt install bwa -y https://excellmedia.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2 tar -xvf bwa-0.7.17.tar.bz2 make