Hi,

The second problemis solved too.
Just for information, the comment ''entree dans bwa wapper'' was printed in stderr . So , either you replace


sys.stderr.write('entree dans bwa wapper')
by print("entree dans bwa wapper")

or you set  " # sys.stderr.write('entree dans bwa wapper')" in comment to avoid 
to display SAM file in red.

Faithfully,
Sarah Maman



Sarah Maman a écrit :
Hi,

This problem bellow is solved thanks to an eccho on $PATH and $DRMAA_LIBRARY_PATH.
I have modified ~/.bash_profile  file to define these two variables.

I just have another questio n about BWA : I try to map with BWA for Illumina (reference and fastqsanger file) but I have this message :
BWA run on single-end

An error occurred running this job: entree dans bwa for illumina
BWA Version: 0.6.1-r104
BWA run on single-end dataEpilog : job finished at ven avr 6 14:16:01 CEST 2012
entree dans bwa wapper

Thanks in advance,
Sarah Maman


Sarah Maman a écrit :
Hi Nate,

When I operate on Genomic Intervals → Get Flanks. The user interface for the tool will appear in the center panel. Make sure the dataset 2: UCSC Main... is selected and set Length of Flanking region to 1000 to create intervals 1000bp upstream of each gene.
I have this error :

Tool execution generated the following error message:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched

The tool produced the following additional output:

Skipped 2 invalid lines starting with #40094L "chr5_h2_hap1 281 935 NM_022909 0 + 281 377 0 1 654, 0,"
Location: Upstream, Region: whole, Flank-length: 1000, Offset: 0
Epilog : job finished at ven avr 6 13:59:08 CEST 2012


Moreover, when I Map with BWA for Illumina ( genome ref and fastq fatsqsanger format ), I have this error :

Tool execution generated the following error message:

entree dans bwa wapperThe alignment failed.
Error aligning sequence. /bin/sh: bwa: command not found

WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched

The tool produced the following additional output:

entree dans bwa for illumina
Could not determine BWA version
Epilog : job finished at ven avr 6 14:04:13 CEST 2012


Could you please help me ?

Thanks in advance,
Sarah Maman






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