makefile loop

loop

10M.2.Trinity.fasta 10M.5.Trinity.fasta 10M.10.Trinity.fasta 10M.20.Trinity.fasta raw.10M.Trinity.fasta \
10M.2.Trinity.fasta.pslx 10M.5.Trinity.fasta.pslx 10M.10.Trinity.fasta.pslx 10M.20.Trinity.fasta.pslx raw.10M.Trinity.fasta.pslx \
10M.2.Trinity.fasta.pep 10M.5.Trinity.fasta.pep 10M.10.Trinity.fasta.pep 10M.20.Trinity.fasta.pep raw.10M.Trinity.fasta.pep \
10M.2.xprs 10M.5.xprs 10M.10.xprs 10M.20.xprs raw.10M.xprs: 10M.left.2.fq 10M.left.5.fq 10M.left.10.fq 10M.left.20.fq 10M.right.2.fq 10M.right.5.fq 10M.right.10.fq 10M.right.20.fq
  for TRIM in 20 2 5 10 0; do \
		$(TRINITY)/Trinity.pl --full_cleanup --min_kmer_cov 1 --seqType fq --JM $(MEM)G --bflyHeapSpaceMax $(MEM)G \
		--left 10M.left.$$TRIM.fq --right 10M.right.$$TRIM.fq --group_pairs_distance 999 --CPU $(CPU) --output 10M.$$TRIM; \
##FL Reconstruction
		$(TRINITY)/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --target $(MUS) --query 10M.$$TRIM.Trinity.fasta; rm *maps *selected *summary; \
##ORF ID
		$(TRINITY)/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl --CPU $(CPU) -t 10M.$$TRIM.Trinity.fasta \
		--search_pfam $(PFAM); \
		rm longest_orfs* *gff3 *dat *scores *cds *bed *inx; mv best_candidates.eclipsed_orfs_removed.pep 10M.$$TRIM.Trinity.fasta.pep; \
##Mapping and eXpress
		bowtie2-build -q 10M.$$TRIM.Trinity.fasta index; \
		bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) | express -o 10.$$TRIM.xprs -p8 10M.$$TRIM.Trinity.fasta >>10M.$$TRIM.mapping.log ; rm index* ; done