bash - pass values from a file as a Makefile variable -


i use values file pass command in make. problem context passing set of ids fetch proteins ncbi using eutils cli. thought of using process substitution pass file location , need string. trying set local bash variable , use in make step cannot work. hints appreciated.

zachcp

shell := /bin/bash   # efetch 1 id test1.txt:     efetch -db protein -id 808080249 -format xml >$@  # efetch two, comma-separated ids  test2.txt:     efetch -db protein -id 808080249,806949321  -format xml > $@  # put ids in file.... data.txt:     echo "808080249\n806949321" > $@  # try call ids process substitution. # doesn't expand before being called trips error... test3.txt: data.txt     efetch -db protein -id <(cat $< | xargs printf "%s,") -format xml > $@  # try set , use local bash variable test4.txt: data.txt     ids=`cat $< | xargs printf "%s,"`     efetch -db protein -id $$ids -format xml > $@

text3.txt work if use $(...) or `...` instead of <(...)

test3.txt: data.txt     efetch -db protein -id $$(cat $< | xargs printf "%s,") -format xml > $@

text4.txt fails because each line executed in different shell process, variable set in first line out of scope in second one; work if put both statements on same line:

test4.txt: data.txt     ids=`cat $< | xargs printf "%s,"`; efetch -db protein -id $$ids -format xml > $@

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