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WGLab / SeqMule

Automated human exome/genome variants detection from FASTQ files
http://seqmule.usc.edu
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Venn diagram is not downloaded #135

Open clwan opened 8 years ago

clwan commented 8 years ago

When I run seqmule with command line: seqmule pipeline -a /home/storage2T/ChanglinWan/SeqMule-master/example/input/normal_R1.fastq.gz -b /home/storage2T/ChanglinWan/SeqMule-master/example/input/normal_R2.fastq.gz -prefix example -N 2 -capture default -threads 4 -e -jmem 10000m It told me the error: Venn diagram is not installed and need manual installment. So I downloaded VennDiagram_1.6.17.tar.gz and unzip it on the ./bin/secondary folder. After that I run the above command again. And the problem is still not solved. So I want to know how can I integrate Venn diagram manually or is there other way to solve this problem? Thanks

yunfeiguo commented 8 years ago

Hi @wayne0422,

Please upgrade your seqmule with 'seqmule update --git', re-run your command and send me the entire stdout/stderr information. Thanks.

Yunfei

clwan commented 8 years ago

Thanks @yunfeiguo image image

This is my result. Not sure is it the information you need. Thanks for your help.

yunfeiguo commented 8 years ago

Hi @wayne0422, the message shows that 'Rscript' is not found. Please install R and put path to its executable Rscript in your PATH environment variable. Thanks.