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I have a bash script which outputs calls to my make file.

#!/bin/bash mylist=( 'SAMPLES_OUT=$(call list_samples,AON_9,NT_1,SC_17) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me1‌​.gff' 'SAMPLES_OUT=$(call list_samples,AON_10,NT_2,SC_18) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me2​.gff' 'SAMPLES_OUT=$(call list_samples,AON_11,NT_3,SC_19) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me3​.gff' 'SAMPLES_OUT=$(call list_samples,AON_12,NT_4,SC_20) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me4​.gff' 'SAMPLES_OUT=$(call list_samples,AON_13,NT_5,SC_21) GFF=/data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me5​.gff' ) for SAMPLES_out in "${mylist[@]}"; do make -f make_gene_read_count.mk -n SAMPLES_OUT=\'${SAMPLES_out}\' done

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 trying to pass 2 variables out of the same array to my makefile but this does not seem to work properly as well if I do it like this in my bash scripts array 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'

Unfortunately it seems that makefile cannot deal with this kind of constructs. How can i pass both variables to my makefile without any command line problems. So how to circumvent $(call) been seen as a command line call. The 2 variables i want to pass to the makefile are GFF and SAMPLES_OUT.

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Bash doesn't support nested arrays or any other complicated data structures.

As the number of arguments is known, though, you can create two arrays, one for each argument:

#!/bin/bash samples=( '$(call list_samples,AON_9,NT_1,SC_17)' '$(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)' '$(call list_samples,AON_13,NT_5,SC_21)' ) gff=( /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me1‌​.gff /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me2​.gff /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me3​.gff /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me4​.gff /data/DIV5/SASC/project-013-motor/analysis/runs/BWA_chipcap/BAMS/GFF/H3K4me5​.gff ) for (( idx=0; idx<${#samples[@]}; ++idx )) ; do make -f make_gene_read_count.mk -n SAMPLES_OUT="${samples[idx]}" GFF="${gff[idx]}" done
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  • Thanks again for this clear explanation and help. Can i assume that the first gff file will be linked to the first sample file? Since i need to make sure they match otherwise a wrong file may be created by the makefile. Commented Feb 16, 2015 at 12:14
  • @SanderVanderZeeuw: Yes, they are linked by the position in the array (represented by the $idx variable). Commented Feb 16, 2015 at 13:09
  • sure, nice and clear as always :) Thank you! Commented Feb 16, 2015 at 13:48

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