[ensembl-dev] could not startup EnsemblGenomes

[Nick Langridge]

Hi Gang Chen,

It looks like you need to install samtools on your system (see 
http://samtools.sourceforge.net/)
You should also ensure you have zlib development package installed.

Cheers,
Nick

On 16/02/2013 10:21, ?? wrote:
> Hi All
>
> I've updated EnsemblGenomes to v17, however, I suffered some problems 
> that caused by new perl environment.
>
>
> /usr/bin/perl /usr/local/share/perl/5.10.1/ExtUtils/xsubpp  -typemap 
> "/usr/share/perl/5.10/ExtUtils/typemap"   bam_c184.xs > bam_c184.xsc 
> && mv bam_c184.xsc bam_c184.c
> cc -c  -I"/usr/local/ensembl_bacteria/conf" 
> -I/usr/local/ensembl_bacteria/samtools -D_REENTRANT -D_GNU_SOURCE 
> -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector 
> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g 
>   -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC 
> "-I/usr/lib/perl/5.10/CORE" bam_c184.c
> bam_c184.xs:6:17: error: bam.h: No such file or directory
> bam_c184.xs: In function ?.re_filter_depth?.
> bam_c184.xs:34: error: ?.am1_t?.undeclared (first use in this function)
> bam_c184.xs:34: error: (Each undeclared identifier is reported only once
> bam_c184.xs:34: error: for each function it appears in.)
> bam_c184.xs:34: error: ?.?.undeclared (first use in this function)
> bam_c184.xs:46: error: expected expression before ?.?.token
> make: *** [bam_c184.o] Error 1
>
> A problem was encountered while attempting to compile and install your 
> Inline
> C code. The command that failed was:
>   make > out.make 2>&1
>
> The build directory was:
> /usr/local/ensembl_bacteria/cbuild/build/Bio/EnsEMBL/GlyphSet/bam_c184
>
> To debug the problem, cd to the build directory, and inspect the 
> output files.
>
>  at 
> /usr/local/ensembl_bacteria/ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/bam.pm 
> <http://bam.pm> line 388.
> ...propagated at /usr/local/share/perl/5.10.1/Inline/C.pm line 772.
> BEGIN failed--compilation aborted at 
> /usr/local/ensembl_bacteria/ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/bam.pm 
> <http://bam.pm> line 487.
> Compilation failed in require at (eval 274) line 1.
> Using a hash as a reference is deprecated at 
> /usr/local/ensembl_bacteria/eg-plugins/bacteria/modules/EnsEMBL/Web/Document/HTML/FTPtable.pm 
> line 55.
>
> What is the problem? need some help, thanks.
>
> ---Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, 
> P.R.China
> Phone: (+86)512-82782588
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130218/43907c54/attachment.html>