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So i just asked a question : for loop over a list

This works perfectly now and outputs what i need. Now i want to link this to a makefile which should be called per variable in my list like this:

#!/bin/bash
mylist=(
    '$(call list_samples,AON_9,NT_1,SC_17)'
    '$(call list_samples,AON_10,NT_2,SC_18)'
    '$(call list_samples,AON_11,NT_3,SC_19)'
    '$(call list_samples,AON_12,NT_4,SC_20)'
    '$(call list_samples,AON_13,NT_5,SC_21)'
    '$(call list_samples,AON_14,NT_6,SC_22)'
    '$(call list_samples,AON_15,NT_7,SC_23)'
    '$(call list_samples,AON_16,NT_8,SC_24)'
)



for SAMPLES_out in "${mylist[@]}";
do
make -f make_gene_read_count.mk -n SAMPLES_OUT=\'${SAMPLES_out}\'
done

This give me a make error: make_gene_read_count.mk:5: *** unterminated call to function `call': missing `)'. Stop.

While if i put echo in front of the call to make in my bash script it prints them out like this:

make -f make_gene_read_count.mk -n SAMPLES_OUT='$(call list_samples,AON_9,NT_1,SC_17)'
make -f make_gene_read_count.mk -n SAMPLES_OUT='$(call list_samples,AON_10,NT_2,SC_18)'
make -f make_gene_read_count.mk -n SAMPLES_OUT='$(call list_samples,AON_11,NT_3,SC_19)'
make -f make_gene_read_count.mk -n SAMPLES_OUT='$(call list_samples,AON_12,NT_4,SC_20)'

If i add one of those echos to the commandline the makefile works perfectly. What am i missing?

This is the makefile:

IN_DIR = /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/namesorted_bams
list_samples = $(shell ls $(IN_DIR)/*$(1)* $(IN_DIR)/*$(2)* $(IN_DIR)/*$(3)* | sed 's/\.namesorted\.bam/\.gene\.read\.count/g')
#SAMPLES_OUT := $(call list_samples,AON_9,NT_1,SC_17)

all: $(SAMPLES_OUT)

GFF := /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me1.gff
GFF_TEMP := $(GFF).temp.gff

$(GFF_TEMP): $(GFF)
    sed 's/\*/./g' $< > $@

%.gene.read.count: %.namesorted.bam $(GFF_TEMP)
    htseq-count -t exon -m intersection-strict -f bam -r name -s no $^ > $@

I am also trying to pass 2 variables to my makefile but this does not seem to work properly as well if I do it like this in my bash scripts list:

'$(call list_samples,AON_9,NT_1,SC_17) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me1‌​.gff'

This is the error i'm getting:

qmake: *** No rule to make target `GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me1.gff', needed by `all'.  Stop.

1 Answer 1

2

You don't want the single quotes to get propagated to the makefile. Don't quote them, and replace them with double quotes - that would keep the variable value as one word in the shell.

make -f make_gene_read_count.mk -n SAMPLES_OUT="$SAMPLES_out"

If you want to pass more variables, separate them by unquoted whitespace:

make VAR1="some value containing $val" VAR2='some other value'
#                                     ^
10
  • thanks, i was really confused by this. Strange is that if i try to run the makefile on command line and it is not between ' ' it will not work, so therefor i thought that this is also the case while running from bash script. Commented Feb 13, 2015 at 13:44
  • I have one more question to you can you tell what would happen if i want for example another variable passed to the make file like this: '$(call list_samples,AON_9,NT_1,SC_17) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me1.gff' Commented Feb 13, 2015 at 14:01
  • 1
    @SanderVanderZeeuw: Questions in comments aren't readable.
    – choroba
    Commented Feb 13, 2015 at 14:04
  • Ooh sure sorry ill add it to my question @choroba It should be in the question now ;) thanks for helping me out Commented Feb 13, 2015 at 14:10
  • @SanderVanderZeeuw: Check the update.
    – choroba
    Commented Feb 13, 2015 at 14:32

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