Which perl library does gasv use?

GoogleCodeExporter commented 8 years ago

GASV runs fine on our server's head node, but when I submit it via a bash 
script I get: 
Can't locate LWP/Simple.pm in @INC (@INC contains: 
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi 
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl 
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi 
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl 
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at 
/nfs/noor/data/sm252/GASV_RELEASE/BAM_preprocessor.pl line 6.
BEGIN failed--compilation aborted at 
/nfs/noor/data/sm252/GASV_RELEASE/BAM_preprocessor.pl line 6.

Looks like I need to install a different library.

Original issue reported on code.google.com by suzanne....@gmail.com on 22 Jan 2011 at 2:57

GoogleCodeExporter commented 8 years ago

The error message is related to accessing the perl module LWP::Simple. This 
module is used by our BAM file preprocessor (BAM_preprocessor.pl) to process 
BAM files located on the web through ftp or http. 

We provided such an example in our BAM Preprocessor README file 
(BAM_preprocessor.txt):
perl BAM_Preprocessor.pl 
ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/pilot_data/data/NA18507/alignment/NA1
8507.SLX.maq.SRP000031.2009_08.bam -SAMTOOLS_PATH /prg/samtools-0.1.6/samtools

There are two options to resolve this difficulty.
(1) If you will *not* be using the BAM Preprocessor for remote files, you can 
simply comment out line 6 of BAM_preprocessor.pl.

But be aware that if you do try to access a remote file, the BAM Preprocessor 
will exit with an error.

(2) To maintain full functionality of the BAM Preprocessor, make sure 
LWP::Simple is installed, by running for example:
perl -MCPAN -e 'install LWP::Simple'

Original comment by sora...@gmail.com on 22 Jan 2011 at 6:29

GoogleCodeExporter commented 8 years ago

Thank you!
This worked out great!

Original comment by suzanne....@gmail.com on 23 Jan 2011 at 2:47

GoogleCodeExporter commented 8 years ago

Thank you for letting us know.

Original comment by sora...@gmail.com on 24 Jan 2011 at 8:48

Changed state: Done

gmarocena / gasv

Which perl library does gasv use? #2