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使用 bash 将 2 个变量传递给 Makefile

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使用 bash 将 2 个变量传递给 Makefile

我有一个 bash 脚本，它输出对我的 make 文件的调用。

#!/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

这是生成文件：

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 $^ > $@

我试图将同一个数组中的 2 个变量传递给我的 makefile，但如果我在 bash 脚本数组列表中这样做，这似乎也无法正常工作：

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

不幸的是，makefile 似乎无法处理这种结构。我怎样才能将这两个变量传递到我的 makefile 而没有任何命令行问题。那么如何规避$(call)就被视为命令行调用了。我想传递给 makefile 的 2 个变量是 GFF 和 SAMPLES_OUT。

答案1

Bash 不支持嵌套数组或任何其他复杂的数据结构。

不过，由于参数数量已知，您可以创建两个数组，每个参数一个数组：

#!/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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