cp /global/projectb/sandbox/gaag/bbtools/tax/latest/tree.taxtree.gz .

#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/plastid.fa.gz out=plastid.fa.gz ow
#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/plasmid.fa.gz out=plasmid.fa.gz ow
#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/mitochondrion.fa.gz out=mitochondrion.fa.gz ow
#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/chloro_mito.fa.gz out=chloro_mito.fa.gz ow
#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/chloro_mito_ribo.fa.gz out=chloro_mito_ribo.fa.gz ow
#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/mito_ribo.fa.gz out=mito_ribo.fa.gz ow
#clumpify.sh -Xmx8g zl=9 fastawrap=4k in=/global/projectb/sandbox/gaag/bbtools/refseqMicrobial/chloro_ribo.fa.gz out=chloro_ribo.fa.gz ow

#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/plastid.fa.gz .
#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/plasmid.fa.gz .
#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/mitochondrion.fa.gz .
#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/chloro_mito.fa.gz .
#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/chloro_mito_ribo.fa.gz .
#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/mito_ribo.fa.gz .
#cp /global/projectb/sandbox/gaag/bbtools/refseqMicrobial/chloro_ribo.fa.gz .

cp /global/projectb/sandbox/gaag/bbtools/silva/latest/both_sorted.fa.gz SSU_LSU_sorted.fa.gz

reformat.sh in=/global/projectb/sandbox/gaag/bbtools/RevisedData/polyA.fa zl=11 out=polyA.fa.gz ow
reformat.sh in=/global/projectb/sandbox/gaag/bbtools/RevisedData/nextera_LMP_linker.fa zl=11 out=nextera_LMP_linker.fa.fa.gz ow

rename.sh in=/global/projectb/sandbox/gaag/bbtools/RevisedData/short.fa out=short.fa.gz prefix=short zl=11 ow
rename.sh in=/global/projectb/sandbox/gaag/bbtools/RevisedData/Illumina_no_adapters.fa zl=11 prefix=artifact out=Illumina.artifacts.fa.gz ow

cp /global/projectb/sandbox/gaag/bbtools/data/phix174_ill.ref.fa.gz .
cp /global/projectb/sandbox/gaag/bbtools/data/lambda.fa.gz .
cp /global/projectb/sandbox/gaag/bbtools/data/lfpe.linker.fa.gz .
cp /global/projectb/sandbox/gaag/bbtools/data/crelox.fa.gz .

reformat.sh in=/global/projectb/sandbox/gaag/bbtools/data/pJET1.2.fasta out=pJET1.2.fa.gz zl=11 ow
cp /global/projectb/sandbox/gaag/bbtools/ribo/latest/riboKmers20fused.fa.gz .
reformat.sh in=/global/projectb/sandbox/gaag/bbtools/data/adapters2.fa out=adapters2.fa.gz zl=11 ow
cp /global/projectb/sandbox/gaag/bbtools/data/truseq_rna.fa.gz .
reformat.sh in=/global/projectb/sandbox/gaag/bbtools/data/mtst.fa out=mtst.fa.gz zl=11 ow
reformat.sh in=/global/projectb/sandbox/gaag/bbtools/data/kapatags.L40.fa out=kapatags.L40.fa.gz zl=11 ow
