I have a big list of programs (samtools,annovar,bra,bedtools etc) in a Programs folder. I have read lots of posts about exporting the path, so that I do not need to identify the whole path to the program from my working folder. However, it still does not work, I guess because I am mixing everything.There is a perl script in the folder variant_effect_predictor which I want to assess from another folders without typing the whole path to this script.I am working on OS X. I added to my ~/.profile following:export PATH=/Users/pics/Desktop/MyDocuments/Programms/ensembl-tools-release-78/scripts/variant_effect_predictor:$PATHsomehow it tells me:pik:Annotation pic$ perl variant_effect_predictor.pl -custom C0066PH1.H3K4me1.ppqt_macs2_broad_v2.20130819.bed.gz,BED_annotation,BED,overlap,1 -i SNPs_vep_input.txt --cache --force_overwrite --symbol Can't open perl script variant_effect_predictor.pl: No such file or directorySo, the path was not exported or added. How can I fix it?
adding PATHs for a bunch of programs
path
When you run it as perl variant_effect_predictor.pl you're telling the perl executable that a script called variant_effect_predictor.pl is located in the current directory and to run it. If it's executable (chmod +x /Users/pics/Desktop/MyDocuments/Programms/ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl) and the inside of the script starts with a shebang (#!/usr/bin/perl or similar on the first line) you should be able to leave the perl part off the begining of the command which will then cause bash to search $PATH which is what you're wanting.