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 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 *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.

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