gusdev-gusdev

[Gusdev-gusdev] error uploading Genbank files

[sucheta T. <su...@vb...>]

Hi,

We have been trying to upload the Genbank data on "trypanosoma cruzi"
using the following option:

ga GUS::Common::Plugin::GBParser
--file=/usr/local/src/gus-related/tcruzi.genbank --debug --gbRel=135
--db_rel_id=1

Prior to this we populated the sres.externaldatabase and
sres.externaldatabaserelease using the values from Chetna's document

We got the following error which was followed by a number of other errors:
--------------------------------------------------------------------------

ERR     LINE=30 unrequireable class     Features        Can't locate
Parse/Yapp/Driver.pm in @INC (@INC contains: /home/apps
/gus/gushome/lib/perl /usr/lib/perl5/5.8.0/i486-linux /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/li
b/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl .) at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN
0> line 92.
BEGIN failed--compilation aborted at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN0>
line 92.
Compilation failed in require at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
line 92.
BEGIN failed--compilation aborted at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
line 92.
Compilation failed in require at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
<GEN0> line 92.
BEGIN failed--compilation aborted at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
<GEN0> line 92.
Compilation failed in require at (eval 33) line 3, <GEN0> line 92.

The file Parse/Yapp/Driver.pm was not found anywhere.

Thanks in advance

Sucheta


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138

Re: [Gusdev-gusdev] error uploading Genbank files

[Steve F. <sfi...@pc...>]

it seems that the genbank parser has a dependency on Parse::Yapp.

This module is available from CPAN 
http://www.cpan.org/modules/01modules.index.html

search that page for yapp to find the download file.

install it in a place that is within your perl path

steve

sucheta Tripathy wrote:

>Hi,
>
>We have been trying to upload the Genbank data on "trypanosoma cruzi"
>using the following option:
>
>ga GUS::Common::Plugin::GBParser
>--file=/usr/local/src/gus-related/tcruzi.genbank --debug --gbRel=135
>--db_rel_id=1
>
>Prior to this we populated the sres.externaldatabase and
>sres.externaldatabaserelease using the values from Chetna's document
>
>We got the following error which was followed by a number of other errors:
>--------------------------------------------------------------------------
>
>ERR     LINE=30 unrequireable class     Features        Can't locate
>Parse/Yapp/Driver.pm in @INC (@INC contains: /home/apps
>/gus/gushome/lib/perl /usr/lib/perl5/5.8.0/i486-linux /usr/lib/perl5/5.8.0
>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/li
>b/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl .) at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN
>0> line 92.
>BEGIN failed--compilation aborted at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN0>
>line 92.
>Compilation failed in require at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
>line 92.
>BEGIN failed--compilation aborted at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
>line 92.
>Compilation failed in require at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
><GEN0> line 92.
>BEGIN failed--compilation aborted at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
><GEN0> line 92.
>Compilation failed in require at (eval 33) line 3, <GEN0> line 92.
>
>The file Parse/Yapp/Driver.pm was not found anywhere.
>
>Thanks in advance
>
>Sucheta
>
>
>  
>