Markupsafe Cannot Be Fetched

Question: Markupsafe Cannot Be Fetched

6.7 years ago by

Sarah Maman • 200 wrote:

Hi Nate, When I operate on Genomic Intervals â 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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modified 6.7 years ago • written 6.7 years ago by Sarah Maman • 200

6.7 years ago by

Sarah Maman • 200

Sarah Maman • 200 wrote:

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 ĂŠcrit :

ADD COMMENT • link written 6.7 years ago by Sarah Maman • 200

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 :

ADD REPLY • link written 6.7 years ago by Sarah Maman • 200

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