Hi, all.

                I set up a local installation of Galaxy and have been trying to reproduce inside it what I had previously accomplished with command-line scripts. One of the tools that I’m using is BWA, so I installed the “Map with BWA Illumina” tool from the tool shed. So far so good. However, when performing alignments at the command-line, I was able to directly input fastq.gz files onto BWA, which doesn`t seem to be possible inside Galaxy.

                Besides saving a lot of storage space, working with gzipped fastq files turned out to give me faster results too, so it’s a “must have” feature for me. When I try to create a BWA task, the form complains that there isn`t any compatible file in my history. If I try to see the files contents, there’s an error message complaining about their encoding. If I gunzip the files, everything works fine.

                Am I falling into any beginner’s dumbness?

                Thanks in advance.

                F.