Question: SAM/BAM To Counts dataset generation errors
1
gravatar for bravobih
4.5 years ago by
bravobih30
European Union
bravobih30 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 COMMENTlink written 4.5 years ago by bravobih30
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 REPLYlink written 4.5 years ago by fubar1.1k

Thank you, we already resolved this problem.

Sorry for the trouble.

ADD REPLYlink written 4.5 years ago by bravobih30

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

ADD REPLYlink written 4.5 years ago by Dannon Baker3.7k
1
gravatar for bravobih
4.5 years ago by
bravobih30
European Union
bravobih30 wrote:

Pysam was not installed in python site-packages directory. After executing pip install pysam everything started to work properly.

ADD COMMENTlink written 4.5 years ago by bravobih30

Thanks for the update!

ADD REPLYlink written 4.5 years ago by Dannon Baker3.7k
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