Question: NGS BWA Installing
0
gravatar for gowdamonish17
2.4 years ago by
gowdamonish170 wrote:

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

next-gen • 8.2k views
ADD COMMENTlink modified 4 weeks ago by gbl160 • written 2.4 years ago by gowdamonish170
1

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.

ADD REPLYlink written 2.4 years ago by Rob90

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.

ADD REPLYlink written 2.4 years ago by gowdamonish170

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.

ADD REPLYlink written 2.4 years ago by genomax62k

Use tar -xvjf bwa-0.7.12.tar.bz2

ADD REPLYlink written 2.4 years ago by genomax62k

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.

ADD REPLYlink modified 4 weeks ago by ATpoint13k • written 4 weeks ago by gbl160

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

ADD REPLYlink written 4 weeks ago by ATpoint13k

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

ADD REPLYlink written 4 weeks ago by gbl160
1
gravatar for Medhat
2.4 years ago by
Medhat8.2k
Texas
Medhat8.2k wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Medhat8.2k
1
gravatar for WouterDeCoster
5 months ago by
Belgium
WouterDeCoster36k wrote:

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.

ADD COMMENTlink written 5 months ago by WouterDeCoster36k
0
gravatar for chen
2.4 years ago by
chen1.8k
OpenGene
chen1.8k wrote:

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

Otherwise, you can download the source, and compile it

ADD COMMENTlink written 2.4 years ago by chen1.8k
0
gravatar for giri.ganesh337
5 months ago by
giri.ganesh3370 wrote:

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

ADD COMMENTlink written 5 months ago by giri.ganesh3370
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