Hi, I am trying to use FastqToSam tool from Picard toolshed. But I keep getting the following exception:
Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollect
Though I have enough space on the disk. It seems some people have the same problem using Picard tools directly e.g. https://www.biostars.org/p/42613/
The problem was that the temp directory was filled up. The suggested solution was to make a folder called tmp in the current directory (mkdir tmp) and then run picard like this:
java -Xmx2g -Djava.io.tmpdir=
pwd/tmp -jar SortSam.jar SORT_ORDER=coordinate INPUT=input.bam OUTPUT=output.sort TMP_DIR=
Now my question is how can I implement the same solution in galaxy.