Need help in shell script to automate this protocol

By krushnach Chandra

This is my protocol and this is how I have to proceed all of them cannot go concurrently until one of them is done

I had this question before got some answer ,but i have still some issues ,so i being with tophat where I have to align the sequenced reads ,so until i align all the reads I cannot go into the next step ,since all those reads are in pair and with condition as my final objective is to compare between various condition.Please dont worry about the biology part it comes at the end as there are lots of reads so what i do now is i have to wait till one of the alignment is done and then issues command for the next read this is very tedious and one read takes around 8-10 hours to get aligned .Therefore i would be really glad if someone can help me in a simple shell script ,any help would be highly appreciated


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