<commit_before>quality_trim:
	for f in *.gz; do \
		gunzip $$f; \
	done
	qsub trim_6147JAAXX_2_1_pf.sh
	qsub trim_6147JAAXX_3_1_pf.sh
	qsub trim_6147JAAXX_6_1_pf.sh
	qsub trim_6147JAAXX_7_1_pf.sh

velveth:
	qsub velveth_6147JAAXX_2_1.sh
	qsub velveth_6147JAAXX_3_1.sh
	qsub velveth_6147JAAXX_6_1.sh
	qsub velveth_6147JAAXX_7_1.sh

velvetg:
	qsub velvetg_line6i.sh
	qsub velvetg_line6u.sh
	qsub velvetg_line7i.sh
	qsub velvetg_line7u.sh

oases:
	qsub oases_line6i.sh
	qsub oases_line6u.sh
	qsub oases_line7i.sh
	qsub oases_line7u.sh

tophat:
	qsub tophat_6147JAAXX_2_1_pf_trim.sh
	qsub tophat_6147JAAXX_3_1_pf_trim.sh
	qsub tophat_6147JAAXX_6_1_pf_trim.sh
	qsub tophat_6147JAAXX_7_1_pf_trim.sh

tophat_ec2:
	cd /mnt/; tophat -p 2 -o line6u_tophat chick3_bowtie2 6147JAAXX_2_1_pf_trim.fastq
	cd /mnt/; tophat -p 2 -o line6i_tophat chick3_bowtie2 6147JAAXX_3_1_pf_trim.fastq
	cd /mnt/; tophat -p 2 -o line7u_tophat chick3_bowtie2 6147JAAXX_6_1_pf_trim.fastq
	cd /mnt/; tophat -p 2 -o line7i_tophat chick3_bowtie2 6147JAAXX_7_1_pf_trim.fastq

index_samfiles:
	cd line6u_tophat; samtools index accepted_hits.bam
	cd line6i_tophat; samtools index accepted_hits.bam
	cd line7u_tophat; samtools index accepted_hits.bam
	cd line7i_tophat; samtools index accepted_hits.bam

extract_reads:
	cd line6u_tophat; \
	for chr in `tail ../chromosomes.list`; do \
	printf "extracting %s..." ${chr}; \
	samtools view -b -o ${chr}.bam accepted_hits.bam ${chr}; \
	done
	
PACKAGES = install_blast install_blat install_gimme install_biopython \
		install_samtools install_seqclean install_cdhit install_khmer_screed \
		install_tophat2 install_bowtie2 install_velvet install_oases
<commit_msg>replace a rel path with an abs path<commit_after>quality_trim:
	for f in *.gz; do \
		gunzip $$f; \
	done
	qsub trim_6147JAAXX_2_1_pf.sh
	qsub trim_6147JAAXX_3_1_pf.sh
	qsub trim_6147JAAXX_6_1_pf.sh
	qsub trim_6147JAAXX_7_1_pf.sh

velveth:
	qsub velveth_6147JAAXX_2_1.sh
	qsub velveth_6147JAAXX_3_1.sh
	qsub velveth_6147JAAXX_6_1.sh
	qsub velveth_6147JAAXX_7_1.sh

velvetg:
	qsub velvetg_line6i.sh
	qsub velvetg_line6u.sh
	qsub velvetg_line7i.sh
	qsub velvetg_line7u.sh

oases:
	qsub oases_line6i.sh
	qsub oases_line6u.sh
	qsub oases_line7i.sh
	qsub oases_line7u.sh

tophat:
	qsub tophat_6147JAAXX_2_1_pf_trim.sh
	qsub tophat_6147JAAXX_3_1_pf_trim.sh
	qsub tophat_6147JAAXX_6_1_pf_trim.sh
	qsub tophat_6147JAAXX_7_1_pf_trim.sh

tophat_ec2:
	cd /mnt/; tophat -p 2 -o line6u_tophat chick3_bowtie2 6147JAAXX_2_1_pf_trim.fastq
	cd /mnt/; tophat -p 2 -o line6i_tophat chick3_bowtie2 6147JAAXX_3_1_pf_trim.fastq
	cd /mnt/; tophat -p 2 -o line7u_tophat chick3_bowtie2 6147JAAXX_6_1_pf_trim.fastq
	cd /mnt/; tophat -p 2 -o line7i_tophat chick3_bowtie2 6147JAAXX_7_1_pf_trim.fastq

index_samfiles:
	cd line6u_tophat; samtools index accepted_hits.bam
	cd line6i_tophat; samtools index accepted_hits.bam
	cd line7u_tophat; samtools index accepted_hits.bam
	cd line7i_tophat; samtools index accepted_hits.bam

extract_reads:
	cd line6u_tophat; \
	for chr in `tail /mnt/chromosomes.list`; do \
	printf "extracting %s..." ${chr}; \
	samtools view -b -o ${chr}.bam accepted_hits.bam ${chr}; \
	done
	
PACKAGES = install_blast install_blat install_gimme install_biopython \
		install_samtools install_seqclean install_cdhit install_khmer_screed \
		install_tophat2 install_bowtie2 install_velvet install_oases

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