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/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_2.0/src). 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     connection
Calls: 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 INFILE_COUNTS.tab and INFILE_CONDITIONS.tab
(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.