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Question: SAM/BAM To Counts dataset generation errors
1
gravatar for bravobih
4.5 years ago by
bravobih • 30
European Union
bravobih • 30 wrote:

When trying SAM/BAM to Counts I get the following error message:   pysam not installed; please install it

But a) pysam was not in this tool dependencies;
       b) pysam/0.7.7 is already installed

 
galaxy • 1.9k views
ADD COMMENT • link •
written 4.5 years ago by bravobih • 30 
Is that https://testtoolshed.g2.bx.psu.edu/view/fubar/htseq_bams_to_count_matrix or something else?

If it's mine, are you running the latest Galaxy code? What does

hg tip

say?
ADD REPLY • link written 4.5 years ago by fubar ♦ 1.1k

Thank you, we already resolved this problem.

Sorry for the trouble.

ADD REPLY • link written 4.5 years ago by bravobih • 30

No trouble, but if you're able please post more details about the resolution so that it might help others with similar problems.

ADD REPLY • link written 4.5 years ago by Dannon Baker ♦ 3.7k
1
gravatar for bravobih
4.5 years ago by
bravobih • 30
European Union
bravobih • 30 wrote:

Pysam was not installed in python site-packages directory. After executing pip install pysam everything started to work properly.
ADD COMMENT • link written 4.5 years ago by bravobih • 30

Thanks for the update!

ADD REPLY • link written 4.5 years ago by Dannon Baker ♦ 3.7k
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