readItAndKeep --ref_fasta /Volumes/Aura/Mus_musculus.GRCm39.dna.primary_assembly.fa \
 --reads1 trimmed_255-001_S1_L001_R1_001.fastq --reads2 trimmed_255-001_S1_L001_R2_001.fastq -o out

kneaddata --input1 255-001_S1_L001_R1_001.fastq.gz --input2 255-001_S1_L001_R2_001.fastq.gz -db /Volumes/Aura/bowtie_C57BL_db --output kneaddata_output --trimmomatic ~/Documents/GitHub/Trimmomatic/dist/jar -t 12 --sequencer-source none


kneaddata --input1 trimmed_255-001_S1_L001_R1_001.fastq --input2 trimmed_255-001_S1_L001_R2_001.fastq -db /Volumes/Aura/bowtie_GRCm39_DB --output kneaddata_output -t 12 --bypass-trim --bypass-trf

http://yum.baseurl.org/download/3.4/yum-3.4.3.tar.gz