SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Runs Of Homozygosity- vcftools clarissaboschi Bioinformatics 0 12-01-2014 05:53 AM
Issues with Fst from vcftools deancastillo Bioinformatics 7 11-25-2014 03:07 AM
VCFtools output after comparison bio_informatics Bioinformatics 0 09-13-2014 07:41 PM
alternative to vcftools for vcf v4.1 Rcucullatus Bioinformatics 5 09-17-2012 11:32 AM
vcftools to annotate SNP rururara Bioinformatics 0 03-31-2011 07:47 AM

Reply
 
Thread Tools
Old 09-03-2015, 10:50 AM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default vcftools install on 14.04.3

I am installing vcftools from github and have two questions:

1. where do I put the samtools1.2 folder so that the tabix and bgzip index can be used.

I added it to path but am not sure where i should put the download.

2. I am following the install guide as posted on github and not able to do the ./configure or make.

Code:
 bash: ./configure: No such file or directory
Code:
 make: *** No targets specified and no makefile found.  Stop.
Thank you .

EDIT:

I was able to do the ./configure and make but get an error doing the make install

Code:
Making install in src
make[1]: Entering directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src'
Making install in cpp
make[2]: Entering directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
make[3]: Entering directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
 /bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c vcftools '/usr/local/bin'
/usr/bin/install: cannot create regular file ‘/usr/local/bin/vcftools’: Permission denied
make[3]: *** [install-binPROGRAMS] Error 1
make[3]: Leaving directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src'
make: *** [install-recursive] Error 1

Last edited by cmccabe; 09-04-2015 at 08:45 AM. Reason: added edit with different error
cmccabe is offline   Reply With Quote
Old 09-05-2015, 03:16 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

Did you try?

Code:
$ sudo make install
GenoMax is offline   Reply With Quote
Old 09-05-2015, 03:51 AM   #3
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default

Yes I did and that worked. I have downloaded tabix and added that to path and will add the Perl5 next, then I should be done. There was no bin folder created as the manual said but we will see. Thanks .
cmccabe is offline   Reply With Quote
Old 09-05-2015, 08:38 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

If there was no /usr/local/bin on your computer then you can make that folder yourself (with sudo). It is a good idea to install or softlink non-system packages that you install into this folder as a common entity present in your $PATH.
GenoMax is offline   Reply With Quote
Old 09-05-2015, 09:14 AM   #5
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default

There is a /usr/local/bin does that not need to be added to path? I have added the tabix to path:

Code:
 echo 'export PATH=$PATH:/home/cmccabe/tabix-0.2.6' >> ~/.bashrc
and now am at the step where I add PERL5 to path

Code:
 export PERL5LIB=/home/cmccabe/Desktop/ngs_analysis/vcftools-0.14/src/perl
or
Code:
 export PERL5LIB=/home/cmccabe/tabix-0.2.6/perl
Not sure which to use?

Will vcftools be usable then? Thank you .

Last edited by cmccabe; 09-05-2015 at 09:16 AM.
cmccabe is offline   Reply With Quote
Old 09-05-2015, 07:44 PM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

You don't have system Perl? http://askubuntu.com/questions/53068...r-ubuntu-14-04
GenoMax is offline   Reply With Quote
Old 09-05-2015, 10:05 PM   #7
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default

No I do not, I will load that but is that whats needed for the PERL5? I am learning ubuntu and how to best utilize it. Thank you .
cmccabe 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 12:11 PM.


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