SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
The problem of installing samtools on mac louis7781x Bioinformatics 2 07-06-2011 09:57 AM
Samtools pileup Consensus with 0.1.12a version srividya Bioinformatics 1 05-23-2011 07:16 AM
BWA 0.5.9rc1 juan Bioinformatics 3 05-17-2011 11:46 AM
BWA - samtools problem genelab Bioinformatics 2 07-02-2010 11:13 PM
BWA - Samtools problem joa_ds Bioinformatics 18 11-08-2009 06:55 PM

Reply
 
Thread Tools
Old 01-14-2011, 12:52 AM   #1
ketan_bnf
Member
 
Location: India

Join Date: Oct 2010
Posts: 59
Default samtools-0.1.12a and bwa-0.5.9rc1 installing problem on fedora14

Hi all,

Recently i upgraded my fedora11 to fedora14. I have installed gcc-4.5.1-4.fc14.i686, zlib-1.2.5-2.fc14.i686 using yum FYI.

earlier on fedora11 samtools-0.1.12a/bwa-0.5.9rc1 was suuccessfully worked.

Now after upgrading when i apply

orf@bnf samtools-0.1.12a]$ make

i am getting this error

make[1]: Entering directory `/home/orf/samtools-0.1.12a'
make[2]: Entering directory `/home/orf/samtools-0.1.12a'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
In file included from bgzf.c:36:0:
bgzf.h:30:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/orf/samtools-0.1.12a'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/orf/samtools-0.1.12a'
make: *** [all-recur] Error 1

when i typed samtools, system asked me to automatically install samtools, so at present i have samtools-0.1.8 (r613) older version, i want to install latest version, How?

[orf@bnf samtools-0.1.12a]$ samtools
bash: samtools: command not found...
Install package 'samtools' to provide command 'samtools'? [N/y] y

same thing is happening with bwa installation, installed typing bwa, system prompt me to install bwa, so having older version of bwa-0.5.8c (r1536) and want to install latest version bwa-0.5.9rc1. When compiling latest version with make,

orf@bnf bwa-0.5.9rc1]$ make
make[1]: Entering directory `/home/orf/bwa-0.5.9rc1'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/orf/bwa-0.5.9rc1'
make[1]: Entering directory `/home/orf/bwa-0.5.9rc1/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/orf/bwa-0.5.9rc1/bwt_gen'
gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
utils.c:32:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [utils.o] Error 1

[orf@bnf samtools-0.1.12a]$ bwa
bash: bwa: command not found...
Install package 'bwa' to provide command 'bwa'? [N/y] y

Pls write me some solutions
Thanks,
ketan_bnf is offline   Reply With Quote
Old 01-14-2011, 01:01 AM   #2
jkbonfield
Senior Member
 
Location: Cambridge, UK

Join Date: Jul 2008
Posts: 146
Default

It looks like you're missing the zlib development package. Try "yum install zlib-devel" on a root command line to get it.

These packages really need a configure script to check such things.
jkbonfield is offline   Reply With Quote
Old 01-14-2011, 06:39 PM   #3
ketan_bnf
Member
 
Location: India

Join Date: Oct 2010
Posts: 59
Default

I installed zlib-devel and ncurses-devel and it worked well.

now using latest versions of samtools and bwa.

Thanks for your help.

Regards.
ketan_bnf is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:27 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO