Hi !
I'm trying to execute Galaxy DESeq2 on datasets created in other steps.
The script executed is *deseq2-hts.sh* (placed at shed_tools/
The first two steps - "Data preparation" and  "Read counting" are executed
without problems, but the 3-rd step - "Differential testing"
reports an error
*Error in file(file, "rt") : cannot open the     connectionCalls:
read.delim -> read.table -> file"*
The error comes from script *difftest_deseq2.R* - it is getting three
command arguments (and they are right) and attempts to read files
(where INFILE - the second argument.)
But the problem that these two files are never created in the
database/files/NNN !

Where can be the root of the problem?

It is a local installation of Galaxy
OS - CentOS 6.5 with all updates.

[image: Israel Bravo on about.me]

Israel Bravo

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